How to Run Payroll

How to Run Payroll


Start a new payroll

1. Payroll > Payroll Tasks > Run a New Payroll

2. If you use different pay frequencies (such as Weekly and Biweekly), select the pay frequency for this payroll.  By default the most frequent pay frequency will display. 

3. If your business has more than one location, you can filter employees by location and run payroll only for the locations you selected.

4. The period start and end dates will be pre-filled based on your last payroll. This is the date range of time worked.  You can change these dates, if needed.  If you do not want to use pre-filled dates, click the “Show Advanced Options” link and choose “No” for “Prefill Payroll Dates.”

5. Enter the pay date.  As with period start and end dates, the pay date will be pre-filled based on your last payroll, and can start with a blank field by choosing “No” to “Prefill Payroll Dates” under the “Show Advanced Options” link.  This is the date your employees are scheduled to receive their pay. Note that the pay date must be after the latest of these three dates:

  • the date of your company’s most recent tax filing (if you are a Full Service Payroll customer),
  • the date of your company’s most recent payroll history entry, or
  • the date your company was set up

6. By default, the payroll includes all scheduled deductions and contributions. To skip deductions or contributions for everyone, click the “Show Advanced Options” link and a list will display. Check off each item to skip for this payroll.

7. If you offer direct deposit and want to turn off direct deposits to distribute live paper checks, click the “Show Advanced Options” link and select “Yes” to Turn Off Direct Deposits.

All active employees will appear on the Payroll Entry screen, grouped by Hourly and Salary.  If an employee is missing any required information, you must fill in the missing info before you can pay that person, but you can still run payroll for the rest of your employees.

Enter employee hours and money.

  • To pay each hourly employee, enter the number of regular and overtime hours, plus any additional hours or money.
  • To pay salary employees, their “Pay?” box is automatically set to “Yes” and included in the payroll. You can change the “Pay?” box to “No” to prevent a salaried employee from receiving their regular pay.  In most states, you don’t have to enter hours worked for salaried employees, but you may choose to for tracking purposes.  Some states do require hours entered for salaried employees for tax purposes.  Entering additional hours will not affect the employee’s salary, but entering additional money will add to their total wages.

Note:  All active Hours and Money Codes appear the worksheet.  To change what appears here, go to Settings > Payroll Settings > Hours & Money Codes and choose the Frequently Used Hour and Money codes.  To activate or inactivate a code, click “Edit” and check or uncheck the Active box.

You have the option to tax money at the supplemental tax rate determined by the IRS.  Check the Supplemental Flat Rate Tax checkbox that appears under the selected money type.  For more information on taxes for supplemental pay, see “How to Tax Supplemental Pay.

Click “Save Entries” to save your changes at any time.

To stop the payroll process and finish it later, click Save Entries.  If you save this payroll and leave this page, you will see a “Finish Payroll” link on the Payroll left menu, reminding you to finish this payroll.  You can also click “Clear Entries” to delete all your entries on this page and start over.

Click the “Next Step” button.

Proceed to Step 2 – Approve Payroll.


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