When you add a new pay run, the first thing it will ask you for is the pay period, the pay period end date and the payment date.

It is important that you get this correct because there is no way to rectify it later (you do have the option to delete and redo the pay run though).
When selecting the dates, also keep in mind that the payment date determines what financial year the payment will fall in.
Once you’ve got the correct rates, click ‘Let’s Start’.