Check in at the hotel is 3PM but you can get your room card as soon as you arrive and this is what you need to go to Atlantis....u take that over there and they give you the wristbands and towels. We got lucky and we were in port until 1:00 AM so we went to the room after the waterpark and used it to shower and such but most people just check in and check right out only to get the pass. We never even checked out, we left the room card open for the day so we could use the room card for the locker rentals and anything else we needed as we didn't want to bring our credit card with us to the waterpark.
As far as staying overnight that depends on when your ship sails...I am pretty sure that they recommend being back on the ship no later than 1 hour prior to sailing, one time it was only 1/2 hour but I can tell you that I have been less than 2 minutes til sailing time RUNNING down the pier to the ship and had them close the doors as we got on...we got a talking to about that! They will leave without you and not feel sorry for you, so I don't recommend being too late, but Senior Frogs can be alot of fun and you do lose track of time!