hey there,
im not certain, but i believe that the entry requirement wil stand the same, whatever point you enter the course. Your best option is to ring the university and speak to them. You are still young, so you still have time to sort everything out if needs be, wether you need to resit the gcses or whatever.
The ATPL theory uses fairly high level GCSE/basic AS mathematics, but many groundschool courses are based around the fact that not everyone will have the maths qualifications that others do. Some schools provide a week at the start where you concentrate on the maths knowledge that will be needed during the ground school.
If I was in your situation, I'd contact the uni, if you can still get on the course id do it that way, rather that doing atpl and then apply.
C89