I've stayed in both Atlantis and the AFT accommodation. Atlantis was much nicer as you'd expect being a resort style hotel. AFT accommodation is simple housing, you don't miss out on anything.
My only advice would be to stay in the accommodation organised through AFT as that way you share with other AFt students. This makes studying much better as you have others to bounce off of and also an excellent way to develop relationships and widen your network......