I just went through the process of trying to set up a 3 line family plan with AT&T pre-ordering. I actually wasn't able to do it on the apple store at all--after waiting two hours for the eligibility check, I just went via AT&T's website and had absolutely no issues. It lets you select what models you want for each line / customize data / etc.
And, from what I can see of the apple store ordering now, when I tried again to start a new AT&T family plan it gave me a screen saying that I would need to go in-store in order to do so--essentially, wait in line and not even have a phone reserved.
So, I would recommend going straight to AT&T, but maybe later in the day Apple will be easier.