If you are wanting to pay a bonus you need to create a pay category and name it something like 'Bonus'. To create a pay category follow this article.
Once you have created this pay category you will need to Create a new pay run. You will need to use the 'Add Earnings' option on the 'Actions' button within the employee record in the pay run and select the 'Bonus' pay category to pay it, remember to select the amount of units in the pay run, if no units are applied then the bonus wont apply to the pay run, if you select two you will get two bonuses for that employee etc.