This is copied from my trip report:
Here is what we did:
There are two ways to do this. You can wait until the day you arrive and check with the Atlantis to see if they have any "day rooms" available. In the past the price has been $ 150 - $ 200 per room depending on the time of year. They won't do this ahead of time. If you call ahead of time you will get a different answer from every operator. From previous Dis boards experience and from all the calls made to the hotel - I could not find any way they would let you book a day room prior to your arrival date. You get 4 wristbands per room, which allows you to use all the pools, waterslides and the beach. It also gives you access to the "The Dig" their huge aquarium. I think you have to check out by 6. Some people call when they get to port, calls can get expensive from the ship, some people head over and check at the desk. Now the Atlantis is huge they have three separate hotels with different areas to check in. Some people have had to go to all three desks to see if they have availability.
The other way to do this is to get a regular overnight room. The Comfort Inn and Suites on Paradise Island has an agreement with the Atlantis to use all their facilities. It tends to be cheaper than booking directly Atlantis. The Comfort Inn is right across the street. I had booked a room (kept watching the rate as it went down just before we left) I think we paid $192.00 plus tax.
(Height of season When I check back the Atlantis was actually booked. Rob and Amber of TV reality shows had just gotten married on Saturday we where there on Monday it was very busy.) It would have cost us about the same if not more if we did the Disney excursion. With the excursion we would not have been able to use the pools or waterslide. If found the best rate for the Comfort Inn at:
http://www.smartertravel.com/hotel/mb.php?id=1417
Now they have I think a 3-day cancellation policy. So if the weather is bad or if the ship does not dock in Nassau for some reason you are out of luck and have to pay for the room. I kept checking the long-range weather forecast before we left just to get an idea.
When we got off the ship in Nassau we took a taxi to the Comfort Inn Paradise Island. Cost was $ 4.00 per person. Kids under 3 were free.
There is also a water taxi you can take but we did not do this. We went to front desk got a pass to get wristbands over at the Atlantis. There was no room ready. (I didn't think there would be) We had worn our bathing suits and brought a change of clothes. We walked over to the Atlantis were we got our wristbands and towels. We spent the whole day enjoying the pools and slides. I had brought sandwiches from room service on ship to have a picnic lunch. Found out later you are not suppose to bring food off the ship -Around 3 pm we went though the Digs and headed back to the Comfort Inn. We got our room - cleaned up and check out. We were in the room less than 40 minutes.
I think it was worth it the kids had a ball. We had stayed at the Atlantis before so I knew what we wanted to do. The resort is so big it can be overwhelming. It did have trouble finding chairs around the pool. Last time we were there in May we didn't have but this April it was crowded. They are adding two new towers so part of the resort is under construction. This didn't affect the pools however.
Hope this helps
Let me know if you have any more questions.
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Full trip report at:
http://www.disboards.com/showthread.php?t=812373&page=2&pp=15
Sounds like it was money well spent. 
