To run a bonus payment for an employee, use a bonus calculator:
Go to your employee’s page
At the bottom of the overview under "Modeling", select one of these options:
Bonus Tax Percent Calculator
Calculate withholding using supplemental tax rates on special wage payments (not applicable in AZ, CT, DE, HI, KY, LA, MA, MS, NJ, UT, WY, Washington DC, and Puerto Rico)
Bonus Tax Aggregate Calculator
Calculate withholding using the last paycheck amount on special wage payments
Run the calculation and then click "Save to history"