We did Atlantis on our own and booked a room at the Comfort Suites, adjacent to the Atlantis. Good thing is that this is a MUCH cheaper option than booking at Atlantis and they give you a wrist band so you can use the slides, water park, etc. Bad thing is that Comfort is a dump(really not that big of a deal since we didn't 'stay' there) worst thing is that we went last year in Nov and it was COLD and further, many of the slides just weren't open.
My advice is to SKIP Atlantis altogether. It is a waste unless you are going in the summer when everything is open. Nassau is a DUMP too, very very dirty and the people are scummy..
We are going on the 7 night Western Cruise in Nov and can't wait. If we went on the 4 night again we would just stay on the ship (except for CCay day!). The ship and CCay is AMAZING!!!!!!! Best vacation ever.