Thanks for all the kind words! I'm glad all my typing's not in vain...

I'll try to answer as much as I can.
For the Comfort Suites, we booked it as soon as we knew we were going on the trip. We checked the pricing at Atlantis first but at this time of year the prices were more than what we found at the Comfort Suites. We checked in at around 10:00 AM and we were encouraged to use the facilites next door right away. To be honest, once we paid for the room I don't think they really cared if we used it or not. At this point I am sure they are so used to all the cruise passengers (that's including other ships as well) that go through the hotel each day that offering the Atlantis privileges has basically become a cash cow for them. They could basically turn many of the rooms over twice in one day and make twice as much on each room.
With that being said, I definitely encourage anyone considering doing this to book early. When we arrived, there were many other cruise passengers already there who wound up at the Comfort Suites because their taxi driver gave them the recommendation to try to get a room there for the day. However, the hotel was fully booked and no rooms were available for them, so those poor uninformed walk-ins were out of luck.
As far as booking the room, we booked it online and thanks to the smart DIS posters here we got a link for 20% of the cost of the room. I will be happy to spread the wealth and post it here:
http://www.smartertravel.com/hotel/mb.php?id=1417
Atlantis is an amazing place. First things first, this place is ENORMOUS. If you think you'll do a lot of walking on the ship, you'll do a lot more at Atlantis. There is a ton of gambling space for those interested, and the condition of the resort is kept well. The staff is friendly and very helpful, and you will find someone to assist you just about anywhere. One nice feature of the resort is The Dig, which is a nicely themed walk-through aquarium. Since we had resort privileges we had no problem going though it several times. The big attraction of course is the water facilities, and the place does not disappoint. There are plenty of choices for you there, such as snorkeling, non-motorized watercraft, slides, pools and more. We even saw a scuba class taking place there. The only thing is that the slides are so popular there were huge lines even at 10:00 in the morning. Perhaps you may have better luck than us though. You can get towels there as well as water tubes but you have to pay for those.
I'll try to post more when I finish my long overdue trip report, but hope this helps!