• Pay the bonus in the regularly scheduled paycheques
• Create and use a new income called Bonus. Follow How to create a bonus income in payroll?

 NOTE: 2020.0 and higher have added the option to include 27 and 53 pay periods in the employee record. The calculations will only be correct if the pay periods per year were set correctly for all paycheques starting Jan 1. See How to change pay period number for an employee?