Remember with agility you need to also look for a bold pup, one that is not going to be afraid to investigate and try new things, no good having a little shy thing, so keep that in mind too. I would go for the most forward pup as well as tugging and ball interest.
You have the plus side of raising the litter, you know the characters of the two, pups can learn, but it is easier with a natural interest already there, forget you love them all, put your business head on and choose the pup that will serve your purpose. For a pet I would choose the one you have bonded with, but for agility and flyball I would choose the other, you will bond with that one when she is on her own, but then again, I can't see them

and watch them, so it's hard on a board, use your instincts, they are BC's so you can't go wrong really can you?