We just returned from the 11/04 Wonder and spent the Nassau day at Atlantis.
It was the high light of our trip. We rented a room at the Comfort Suites (175+tax) which gives you full access to the Atlantis pools, slide, aquarium and beach (you are given wrist bands which give you access to everything, including towels). My kids would have been devastated if we went to Atlantis and couldn't use the slides, lazy river and pool (if you book through the cruise line, you don't have access to the pools and slides)
You just grab a cab (at $4/person) outside the cruise terminal and it's about a 5 minute ride to the resort.
Let me know if you need further info