Don't worry. The online application is designed to test your ability to work with a completely unusable computer system to ensure that JPA won't frustrate you for the next 20 years!!!
Seriously though, see if their is an option of 'branches' for officer entry and within that Fly (pilot). If not I'd just give your local AFCO a call - that's what they're there for (and be sure to feedback that the computer system isn't very user-friendly). One or 2 days delay on your application won't make much difference.
All the best