no there will not be two lines at the apple store. There will only be two lines at the AT&T store.
the pre-order process at the apple store doesn't guarantee you a phone, it only allows the purchasing process to go quicker once you get there. iPhones at the apple store will be sold on a first come first serve basis.
the att store WILL have two lines however, but that is because the pre-order process at the att store is different. People who pre-ordered through att have actually already paid for the phone and have their name written on it. Their phone will be waiting for them, hence why att is letting these people be part of a separate line that gets to receive their phone first.