You should setup a new earning code and ensure that the option Non-Periodic Payment is selected.  Assign this code to the employees that you want to issue bonus cheques to.  Create a selection list for the Bonus employees and create timecards with the amounts of the bonuses on them.  Run the Calculate payroll function for this selection list.  Print your checks and post the pay run.   

Another way to go is to enter the Manual checks (instead of timecards) for the bonus amounts and then print the checks.  

The payroll user guide is integrated into the Sage 300 help menu which is accessed by opening any screen and typing F1 on your keyboard. The last released payroll guide released in PDF format was for Sage Accpac ERP 5.5. It is a bit dated, but can be accessed through the Sage KB ID ID:37742. 

Also, if I would recommend the time card since the manual check would require you to manually calculate and enter taxes.