You can set the pay schedule for fortnightly, but this doesn't dictate how often you pay your employees, or what period you pay them. This is only used to help you make sure you don't miss any days of pay.
For example, if you have a pay that is from the 1st of April (with pay schedule set to 2 weeks), you can still choose to pay from 1st to the 15th (15 days), not 1st to the 14th (14 days). The pay schedule is really just trying to make sure that you don't forget to pay someone :).
Is that helpful?