From what I've gathered, Jenna/Melissa/Shana seem to be working against A? They're at least a team of their own, and they don't seem to be working with A. I have a feeling there's more to the NAT-club, and that they play a part of it. Or maybe they're looking for Ali?
A and Alison's "killer" is not the same person (I'm pretty sure about this), so they could have their own reasons for wanting to get a hold of Ali.
Cece helped Alison, I think. Like, keeping track of the girls?
I hope Ezra was A from the beginning, but at this point I'm even doubting if they're going to make him A. They might just do a Toby