We just got back from the 3-day Wonder and after asking many questions about Atlantis on these boards we finally decided to "wing it". We did not book in advance at Atlantis or Comfort Suites instead we took a cab to Paradise Island ($4 per person - no bridge toll. Our cab driver said 5 and under were free) and went to the front desk at Atlantis to inquire about a room. We explained that we really only wanted the room for the day and after conferring with a manager we got a room for $150. We wandered around the lagoons and eventually got wrist bands at a towel stand. Personally, the only time we saw an employee looking for a hotel guest wrist band was at one of the slides. We went down the lazy river twice, did the slides only a few times and went to the beach for about 1/2 an hour. I got stung by a jelly fish and DD got overwhelmed by a couple of waves and lost all interest.
We had packed in ziplocks ham, cheese, rolls, fruit and cookies from the breakfast buffet so we enjoyed a nice lunch in the room. We also showered and got dry clothes on before heading back to the ship (another $4 per person). Total we probably spent about 4 hours at Atlantis.
You said you have a 5 year old - check the child's height because they have to be 48 inches to go down the Mayan Temple slides. My DD was about 2 inches too short and they would NOT allow her to go down. She was quite bummed.
Good luck on making an excursion selection!