Set the schedule on the bonus pay to have a different period ending date than the regular pay type assigned to this employee. 
  1. In the Payroll. select Configuration, Pay Types.
  2. Select the Schedule tab, then mark the button to Pay only in periods with specific end dates.
  3. Schedule a period end date on a day different than the regular pay type assigned to the employee.
  4. Save and Close the record.
  5. Create the payroll calculations using the period end date for the pay type defined in step 1, and only select to create the calculation for this employee.