1. Create a one time pay type for the amount to be paid to the employee. 
2. Add the pay type to the employee record for the next Payroll run. 
Manually adjust the employee's hours on the next Payroll run to equal the expected gross pay plus the amount to be added.
If checks have been cut but not sent out:
1. Void the payment(s)
2. Edit the calculation from the employee(s) record