After reading the DISBoards for months and PMing some DISers, I finally got the courage to give this a try on our 2nd trip to Nassau.
Here's our story:
We were on the June 1, 2008 Wonder.
I booked 2 Comfort Suites rooms with a AAA rate of $152 each for my family and a cousin's family - both families of 4. I reserved the room for the night beginning the date of our arrival in port - even though we would not be staying the night. As we left the ship around 10am, we ran into another family of 4, also headed to Comfort Suites. The night before, I went to the Shore Excursions desk and got a map of Atlantis.
DCL's shore excursions personnel suggested we take a cab instead of the water taxi due to distance from the Comfort Suites.
As you enter Nassau, there will literally be 100s of people standing around offering to take you to Paradise Island, Atlantis, etc. We chose a man that had a sign saying "$4 cab ride to Atlantis". We told him we had 12 in our party, and he took us around to an older model toyota van that seated 12 and even had A/C. (even though the sign had a price, be sure to agree on a price before you ever step foot in the cab!) Be prepared to pay $1 for a token for the toll bridge over to Paradise Island. Our ride cost us $4 per person, and we exited at the door to the Comfort Suites.
We arrived at the Comfort Suites at 10:30am, told the desk clerk that we wanted to check in and out at the same time, and we were ready to go in about 5 minutes. Our $152 rate, ended up at a total of $194. (When you book there is notation for extra $8/pp additional resort fee, plus tax, so I knew it would be close to $200.)
I asked the clerk how many reservations she handled with a check-in and out the same day, and she said there were 60 arrivals like ours just on that day. So, do not be afraid to book this way - they are VERY familiar with the cruise ship visitors.
The clerk gave us a card for each adult with a "paid" stamp. This gets you an armband for the Atlantis activities. With our cards in hand, we headed directly across the street to Atlantis. As you enter the resort, you are on the Beach Towers side. You will head through the lobby and down some stairs to enter the outdoors area of the property. At the Coral Towers Beach hut, (we had to ask directions a couple of times) you will pick up your beach towels and wrist bands.
Even though Atlantis is "across the street" from the Comfort Suites - it is still a 15 minute walk within the resort to get to the Aquaventure, Dig, and Casino areas. The walk is pleasant - with fish exhibits, pool areas, a beach and beautiful landscaping - so it isn't too bad. It was 11:15 when we arrived at the aquaventure area and we headed straight to the popular water slides. They were great! But, the line gets much longer after noon. The kids and the adults loved the slides (ages 14,13,12,10,8) and the youngest, age 6, was only able to ride a small kiddie slide. You must be 48in to ride, and they do measure and enforce this rule.
The pools are beautiful and 2 of the largest are in the waterpark area. Everyone's favorite, though, was the lazy river - a mile ride around the resort - which isn't really all that "lazy". There are some fun rapids, too, but no big drops.
We brought our own bottled water in a small six-pack sized cooler. We shared snack food - $6 nachos, $7 chicken fingers, $4 fries, $4 soda(free refills) and each family spent about $25. They DO NOT TAKE CASH at the food area, so be sure to bring a credit card!
We changed into street clothes and left the resort about 3:20pm. Walked the opposite way of our arrival, to the main Royal Towers resort lobby (much closer) to catch a cab back. Prices are posted and concierge is standing out front and will direct you to a cab - much less intimidating than the ride over!!
Traffic was VERY HEAVY - and we arrived back at the dock area about 3:55pm. Customs agents check your ID and KTTW card - they were quick and pleasant. Once back on board, we headed to Goofy's Galley and the Pizzaria for a real lunch. (perfect timing for us, because we had 8:15 dinner).
We had a great time, made some nice new friends - we actually all stayed together for the entire day - and will definitely do it again!!
Comparison:
Atlantis -on your own
$194 for 2 adults/2 children ages 10 & 14 +
$40 2 cabs rides with tip +
$25 snacks =
$259.
VS
DCL Aquaventure
$
165 per person x 4 = $
660!
a total savings of $400!! 
Just a side note: I would not recommend keeping the room to go back and shower, etc because it is such a long walk. Even if you reserved a room at the Atlantis beach towers (least expensive) the walk will be equally far. Also, the line to check in at the Atlantis Beach towers was EXTREMELY long - there had to be at least 30 people in line. We were the only ones checking in at the Comfort Suites.
Also, next time, we will bring some bagged chips and snacks along
. Your bags are not checked at Atlantis.
We did not bring our cameras along - I didn't want to worry about them getting wet and/or stolen. So, we dont' have any photos - sorry!
Factor in the cost of taxis to/from and the lunch which is included in the DCL excursion. For my family of 4 (my boys are 16 & 15) it wasn't enough savings to get me to book on my own via CS. 
