Answer
To enter pays retrospectively in the program, you will need to go to the Pays tab, then hold down the Last Pay Run button on the left, and skip through to the pay period you'd like to start entering pays from. Once in the pay run you're after, you can edit pays like normal, then, once all relevant pays are complete, you can click Next Pay Run on the right and complete the next pay run, and so on, so forth.
If your employees' names are not in the pay run you skip back to, you can click on Create Pays Wizard to add them into the pay run. If you cannot add certain employees to a past pay run, please see the second paragraph of this FAQ.
It is also possible to edit past pays, though please bear in mind this would be done only in a few specific scenarios, as you do not generally want to edit any values that had been paid out at the time, being that you want to have accurate records of what was paid and accounted for at the time (even if there is a mistake in there).
If you find yourself in a scenario where you need to edit a past pay, you will need to skip back to the pay run in question, click edit pencil icon to the right of the employee's pay you're editing, then click on the little padlock button at the bottom left of the screen to unlock the pay for editing, then proceed as usual.