Run Payroll

Purpose: This help guide will walk you through the three steps of processing your payroll. 

How do I Determine What Employee Data is Included in the Payroll?

Please note that starting the payroll process takes a snapshot of the employee data as of the pay cycle start date. If you have an employee data change that is effective during the pay cycle, it will not automatically be included in the current payroll. Instead, those changes will be effective in the payroll following the effective date. If the change does need to be included in the current payroll, you will need to manually override the changes during step 2 of payroll. Before starting the payroll process, you’ll want to be sure to make any essential changes or additions to your employees prior to running payroll. 

If you forget to make changes before starting payroll, you will need to remove the employee from the payroll and then add them back in once you've made the applicable changes. This can be done in Step 1 of Payroll. 

Employees will only be included if they have active records as of the pay cycle start date.

  1. If an employee has a wage or demographic record end, and a new record starts within the pay period range we will use the record that was effective at the beginning of the pay period for reference of which information to use on the payroll. 
  2. If an employee has multiple active wages due to job tracking, and also has wage or demographic records end and start within the pay period range we will always use the record that was effective at the beginning of the pay period for reference of which information to use on the payroll. Note: These two scenarios may cause an employee to be underpaid. If you need to override this, you can do so in Step 2 of running payroll. 
  3. If an employee is terminated during a pay cycle but was active on the pay cycle start date we will still include them in that payroll run. 
  4. We will check for any new hire dates that fall within the current pay cycle to ensure new hires are not excluded from payroll if they start in the middle of a pay cycle. New hires must also have active wage and demographic effective dates to be included in the current payroll.  

Run Payroll in the Payroll Center

All payroll runs are processed in the Payroll Center using an easy, three-step process. To get started, navigate to the Run Payroll tab found in the Payroll Center. You will see a list of available payrolls with specifics about each payroll including the payroll start and end dates.

1. Run Payroll: If the payroll has not yet been started, you will be able to click "Run Payroll" to begin your payroll run.  Be sure to verify that your pay dates are accurate first. 

If you have already started working on your payroll, you will see options to Continue Payroll or Reset Payroll instead.  

2. Continue Payroll: Choosing to "Continue Payroll" will bring you back to the payroll data you were previously working on. 

If you are using the BambooHR integration and have Autosync, the system will automatically run a sync when you click "Continue Payroll" to make sure there haven't been any new deductions on the company or employee level. If there are, they will be applied to the employee's record. If any errors related to the sync occur, you will see an error message at the top of the screen requiring you to fix the deduction error before you are able to continue the payroll.

3. Reset Payroll: If you have started a payroll run, but have determined that you need to make changes or start over, simply click the "Reset Payroll" button to refresh and restart your current payroll run. A pop-up box will appear asking you to confirm that you understand that this will be resetting your payroll run and you will have to re-enter all changes, including hours worked. Once you click "OK", you can proceed with restarting your payroll run.

If you are using the BambooHR integration and have Autosync, clicking on reset will immediately trigger the running of autosync and then re-open the payroll.

Clicking on any one of the three options (Run Payroll, Continue Payroll, or Reset Payroll) will bring you to a new screen where you will be walked through the three steps of processing payroll.

Run Payroll

  1. Payroll Parameters: At the top of the new screen, you will see the payroll parameters listed including the Payroll Type, Pay Date, Pay Period Start Date, Pay Period End Date, Due Date, and the unique Pay Cycle ID number. 
  2. Search Section: There are search fields available to make it easier to search for specific employees within this payroll cycle. You can search by Wage Type, Department Type, and Tax Type.
  3. Search Box: You can also use the Search box to search for an employee by name or other qualifying factors.
Step 1 - Review and Update Hours and Time Off

Within the first-step screen, there are several features available that will help speed up the payroll management process.

  1. Zero All Wages: By clicking "Zero All Wages" you are able to zero out all regular wages for a specific payout event such as a bonus or commission payroll run.
  2. Get Approved Hours: If you are using TRAXPayroll's Time Sheet feature, you will be able to click "Get Approved Hours." This will automatically import all data from the Time Sheet tab into the current payroll. Note: If you are not using the Time Sheet feature, the "Get Approved Hours" button will not show, but you can key in the hours in Step 1 or use the upload hours feature.

If you are using the BambooHR integration and have Autosync, clicking "Get Hours" will pull Time Off, Holiday, and Time Tracking hours, if applicable, from BambooHR. Double Time hours will populate in the "Other Hours" category.

3.     Add Employee: Click "Add Employee" to include an employee in this payroll who is not usually included or no longer included in payroll. Please note that employees who are not marked to be included in payroll or who do not have active wage and demographic records will not show up in the payroll run and will need to be added manually. If you notice an employee is missing from the payroll run, you can select them from the drop-down list and add them to the payroll run. The employee's wage and demographic record must be active as of the pay date. Only employees who are assigned to the corresponding pay group can be pulled into the payroll run. 

If you are using the BambooHR integration and have Autosync, the system will automatically sync a refreshed list of available employees in the pay schedule to add to the payroll. If an employee who is not currently synced with TRAXPayroll is selected, the entire employee autosync will take place. This experience is the same if you are adding an employee who was previously excluded from the payroll. If any errors related to the employee sync occur, you will see an error message at the top of the screen requiring you to fix the employee errors before you are able to add them to the payroll.

4. Get Uploaded Hours: If you are not using TRAXPayroll's Time Sheet feature, you will be able to upload hours into your payroll run. After your file has been uploaded and confirmed, you will be able to pull the uploaded data into this step of the payroll run.

If you are using the BambooHR integration and have Autosync, you will need to import your hours in BambooHR in order to add them to payroll. This button will show as "Get Hours", allowing you to pull these imported hours from BambooHR into your payroll run.

5. Delete: Clicking "Delete" enables you to remove an employee from the payroll if needed. Note: If an employee's data is incorrect (demographic record, overtime rate, etc.), then you can remove them from the run, update their employee tab, and then add them back using the "Add Employee" feature so that their information is correct for the payroll run. Click "Clear All" if you'd like to uncheck all employees and then you can check the box next to each specific employee you need for the payroll run.

If you are using the BambooHR integration and have Autosync, you will see a link next to Delete on each employee's row for "Update." You can click this button instead of deleting the employee and re-adding them to the payroll when you need to re-sync the employee's information in the payroll run. This will update any revised data that comes from BambooHR on the employee's record in TRAXPayroll. If any errors related to the employee sync occur, you will see an error message at the top of the screen requiring you to fix the employee errors before you are able to update their information in payroll.

6. Review and Make Edits: You can review and make edits to any of the fields in the payroll cycle except those that are greyed out. If the fields are greyed out for an employee, then they do not have a wage rate for that hour type or that time off type is not available on their employee record.

7. Save Changes: If you've made revisions, be sure to click "Save Changes" to make sure all revisions are saved before you navigate away from this page. When you click "Next" to move on to Step 2, TRAX will automatically save any changes made in Step 1.

8. Preview Hours Input Sheet: You have the option to preview your hours entered before moving to the next step by clicking on "Preview Hours Input Sheet." Note: Make sure you click "Save" before choosing to preview or the data will not be included on the report. 

9. Next: Clicking "Next" will save your changes and take you to Step 2.

Step 2 - Review and Update Additional Pay

Step 2 of your payroll run allows you to review and enter any additional pay. If needed, it also allows you to change federal withholding elections to a flat percentage for special circumstances, such as a bonus payout. Extra pay can be added during this step and one-time overrides can also be done. 

  1. Search Section: You can double-click on "Search Section" to expand the search section to include Wage Type, Department Type, and Tax Type. 
  2. Global Payroll Update: Changes to certain items can be made to all employees in the entire payroll run. Keep in mind that these changes are only for the current payroll; they will not affect the employee's permanent record. To get started making changes to the entire payroll run, click "Global Payroll Update." In the Global Payment Update pop-up, you'll have several options available. 
Want to Learn More About Global Payroll Updates?
  • Return to Step 2: At any point, you can choose to "Return to Step 2" without making any global updates. 
  • Additional Pay Expense Section: If employees have recurring pay on their wage records, such as expense reimbursements, it can be removed for the payroll run by clicking on "Update All Additional Pay."
  • Employee Bank Section: You can choose to issue paper checks for all employees by clicking "Update All Printable Checks."
  • Tax Section: The Tax Frequency of the payroll run can be changed from the normal pay period taxing schedule. From the drop-down list, you can choose Annually, Bi-weekly, Daily, Monthly, Quarterly, Semi-annually, Semi-monthly, or Weekly. This is very useful during a bonus run. After you select the Tax Frequency, click "Update All Frequencies" to save your changes. You can also set federal income tax to a flat percentage for all employees,  such as 22% for the supplemental pay rate. Once you have typed in the percentage, simply click "Update All Fed WH" to save your changes.
  • Deduction/Accrual/Garnishment Section: Deductions, garnishments, and hour benefits can be suppressed by choosing the "Yes" radio option next to the appropriate item. Keep in mind that suppressing benefits will prevent manual debits and credits from posting during this payroll cycle. Be sure to click "Update Suppressions" after making your selection.
  • Close: Once you have made all the needed changes, click "Close" to return to Step 2. 

3. Get One Time Deductions: One-time changes can be made to deductions by clicking "Get One Time Deductions." This will pull in any deductions that have been uploaded prior to running payroll. This will only affect the current payroll run. This button will only show if you have imported a file for one time deductions. 

If you are using the BambooHR integration and have Autosync, you will not be able to upload one time deductions when running payroll.

4. Search: You can also use the Search box to search for an employee by name or other qualifying factors.

5. Delete: Clicking "Delete" enables you to remove an employee from the payroll if needed. 

6. Edit: One-time override adjustments can be made on each employee. Click "Edit" next to the employee's name to be taken to the Edit Step 2 screen for the individual employee. Here, you can add extra payments, make one-time changes to update withholding elections, tax frequencies, deductions, etc. Changes made under "Edit" will only affect the current payroll run. 

Want to Learn More About One-Time Override Adjustments?
  • Wage & Extra Pay Section: In these sections, the employee's Wage information will be shown including Wage Type, Overtime Status, Salary, Other Rather, and Overtime Rate. Also, up to three Extra Pay Types can be added for an employee. Enter the amount of Extra Pay and select the Pay Type from the drop-down menu.
  • Timesheet Hours & Additional Information: Entered Regular Hours, Other Hours, and Overtime Hours will be shown in the Time Sheet Hours section. You can also enter Notes under Additional Information. These notes will be added to the employee's pay stub.
  • Federal Withholding & State Withholding & State Unemployment Insurance & Tax Sections: There are four sections where an employee's tax elections and amounts can be changed for the current payroll run. Also, the Tax Frequency of the payroll can be changed to affect taxing if necessary.
  • Employee Bank Section: Employee payment options can be changed here for the current payroll run. If the employee has multiple banks, you can choose to send the money to only one account or you can choose to override the banking information for a printable check.

If you are using the BambooHR integration and have Autosync, the system will automatically sync current bank information when you select "Send money to one account?" This way you will see a current list of the employee's bank account options. If there are any errors that occur during the bank information sync, you will see the associated error message at the top of the screen. The errors will need to be resolved before you will be able to select the corresponding bank for payment.

  • Deduction/Accrual/Garnishment Section: One-time adjustments can be entered during payroll to correct employee deductions and garnishments. 
    • Override Amounts: Override Amounts can be entered here. Enter the amount to be adjusted that includes the current payroll deduction. This amount will be taken in the payroll run instead of the usual deduction amount. If a deduction has been over-collected, enter a negative amount in the Employee Override Amount field.
    • Employer Override Amount: Override Amounts can be entered here. Enter the amount to be adjusted that includes the current payroll deduction. This amount will be taken in the payroll run instead of the usual deduction amount. If a deduction has been over-collected, enter a negative amount in the Employer Override Amount field.
    • Please note that collectible deductions such as garnishments are not allowed to be reversed. 
  • Additional Pay Expense Section: Additional pay and expenses can be deleted or suppressed in this section by clicking "Delete" or checking the "Suppress" box respectively.

Make sure to click "Save" at the top of the page so your revisions will be made to the current payroll run or click "Cancel" at any time to exit this section and return to Step 2 in the Payroll Center.

7. Add Check: Click on "Add Check" to add additional checks for employees. This will add separate paychecks so that they can be taxed differently. 

8. Review and Make Edits to Extra Pay Amounts and Pay Types: To add extra pay types to an employee, enter the amount in the "Extra Pay 1" column, then select the pay type from the drop-down list. Remember, through clicking "Edit" you can add two more Extra Pay Amounts and Types if needed. However, make sure that you save the information entered before clicking edit. 

9. Save Changes: No changes are saved automatically so remember to click "Save Changes" before navigating to any other screens. 

10. Back: Select "Back" if you need to return to Step 1 for any reason. 

11. Preview Additional Pay/Expense: A report of additional pay entries is available to review by clicking "Preview Additional Pay/Expense." Be sure to Save Changes before choosing to preview the report. 

12. Calculate Payroll: Once you have entered any additional pay and have made any necessary changes, click "Calculate Payroll" to move on to Step 3 and finalize your payroll run.

If you are using the BambooHR integration and have Autosync, the system will automatically sync certain information when you click "Calculate Payroll" to move on to step 3. The following information will sync:

  1. Employee Deduction and Company Deduction: This sync will calculate the deduction amount, cap amount, and global limit.
  2. Employee Termination Date: In order to calculate hours on salary employees, we perform a check on employee termination dates. This will sync all employees in the pay schedule to ensure that all termination date information in BambooHR is up to date in TRAXPayroll.
  3. Direct Deposit Information: This will sync the employee bank information. This ensures we have the most up to date bank information for all employees included in the payroll.

If there are any errors that occur during any of the syncs listed above between Step 2 and Step 3, you will remain on Step 2 of payroll to resolve all errors listed. You will not be able to move on to Step 3 until the errors are resolved.

Step 3 - Review and Approve Payroll

In Step 3, you can review the payroll data for accuracy before approving it.

  1. Review Each Employee: Each employee is listed with their wages, taxes, deductions, and net pay. You can easily click on an employee's name to view a PDF of their unapproved earnings statement (pay stub). This makes it easy to review each pay stub for accuracy before finalizing payroll. 
  2. Total to be electronically transmitted: The amount of the payroll debit includes direct deposits, employee and employer taxes, collectible garnishments if any, and fees. Garnishments for tax levies (child support, etc.) can be set up to be collected and paid by TRAXPayroll. They are considered collectible deductions and are included in the payroll debit so we can pay them on your behalf. Uncollected deductions, such as health insurance, 401(k), etc. are not included in the debit. They stay in your bank account for you to distribute as needed. Checks to Print will also not show up under the total debit but will show under the Total Cash Requirement needed to process this payroll. 
  3. Reports: A variety of reports are available to help you review your payroll for accuracy before approving the payroll. All entered data will be preserved. 
  4. Deposit Limit: If a single direct deposit is over $100,000, then NPC will require that the entire amount for the payroll is submitted via a wire. You can see this employee's pay information is highlighted in red so you are aware of the limit. Contact our customer support team prior to your payroll being approved in order to arrange wiring the funds. 
  5. Approve Pay Date: Once you have confirmed that all information is correct, click "Approve Pay Date" to finalize your payroll. Once payroll is approved, the status of the payroll will show as "Pending" until it is processed on the due date. You can approve payrolls in advance of the due date, and they will not be processed until the due date. The pay date is shown on the Approve button for easy reference. On the Approve Payroll Process page, you'll be able to see your pay cycle details and View Pay Cycle Reports. (See below)

If you are using the BambooHR integration and have Autosync, the system will run a sync of all hour benefits and accruals in BambooHR to ensure that all the correct information is used when we upload the final payroll and generate paystubs. If any errors occur with this sync, you will need to resolve them before approving the payroll.

6. Cancel: If changes need to be made, you can click "Cancel." This will take you back to the Payroll Center where you can choose to continue the payroll again and make changes as needed. If you choose to cancel the payroll, all data will remain intact so that you can make the needed changes without losing what you've already entered.

Confirmation Email

Confirmation Email: A confirmation email will be sent to the approver. Other admins can receive the approval email also if they are marked as such in the company users tab. A second confirmation email will be sent to the approver when the payroll is processed by TRAXPayroll.

How do I Reopen a Payroll Run to Make Changes?

If you need to reopen a submitted payroll to make changes, you will see a "Reopen Payroll" button on pending payrolls that will be available until 12 PM Pacific Time on the due date. 

Click on "Reopen Payroll" and you will see a confirmation pop-up to confirm your action.

Once confirmed, you can click "Continue Payroll" to make the necessary changes.

If you need to make a change to a locked payroll run, you can contact our support team to have the payroll reopened. If you have multiple payrolls in your payroll center, please be specific about which one you want re-opened. The Pay Cycle ID is the best way to identify the specific payroll. You can find this six-digit number in the payroll center next to "Waiting for funds to transfer." Please note that there is a $10 fee for reopening a locked payroll. 


What's Next?

Did you miss the payroll processing deadline?

Do you have more questions about payroll?

Would you like to use the sample tax calculator?