Option 1:
Clear all calculation frequencies check boxes when you process the check. Only taxes calculate on the check. Any automatic pays, deductions or fringes do not calculate on the check. If the employee has direct deposit and you need to generate direct deposit for the bonus check, use Option 2 instead.

1. In Payroll, from the Tasks menu, select Enter Checks.
2. Click List, select the time entry view, and then click OK.
3. Click List, select the employee, and then click OK.
4. Type the Period end date and then press TAB.
5. In the Check seq box, select Second and then press TAB.
6. Enter the bonus pay information in the time entry grid.
7. Click Process, clear all calculation frequencies check boxes, and then click OK.
8. Click Chk Info, verify the check amount, and then click OK.
9. Click Accept check.
10. Repeat steps 3 through 9 for each additional bonus check for other employees.
11. Click Finish.

Option 2:
Delete the units and amount on the salary pay ID after you process the check. Also, delete the amount on any other pays, deductions and fringes that you do not want to calculate on the check.

1. In Payroll, from the Tasks menu, select Enter Checks.
2. Click List, select the time entry view, and then click OK.
3. Click List, select the employee, and then click OK.
4. Type the Period end date and then press TAB.
5. In the Check seq box, select First and then press TAB.
6. Enter the bonus pay information in the time entry grid.
7. Click Process, select the calculation frequencies and then click OK.
8. In the time entry grid, select the salary pay ID and then delete the Units and Amount for the salary pay ID.
9. Click Accept line. Click OK when the following message displays: "The row does not have units or amount".
10. Delete the amount for any other pays, deductions or fringes that you do not want to calculate on the bonus check.
11. Click Process, select the calculation frequencies check boxes and then click OK.
12. Click Chk Info to verify the check amounts. Click OK.
13. Click Accept check.
14. Click Finish.

Why are the withholding taxes so high on bonus checks?
How do I set up bonus pays or supplemental wages to be taxed at a specific rate in US Payroll?
How do I enter a bonus check and have only taxes calculate?