You can easily add a commission amount for an employee in regular payroll.
- Click the Run Payroll tab.
- Click Run Regular Payroll.
- Next to your employee, click Other Earnings
- Next to Commission, enter the dollar amount
- Click Save.
- Finish running payroll.
This commission amount will be taxed as regular wages. It will also be seen as a separate line item for commission on the employee's paystub.