We didn't book a room at CS but got a day room at Atlantis...and loved it. From what I have heard you'll get the same perks as everyone that is a hotel guest at Atlantis...and since you already have your reservation booked...you won't have to waste fun time trying to get a day room.
Depending on who is in your group and what your wanting to do...depends alot on if it's worth it. For example you have to be 48" tall or taller to use most of the slides...and for those smaller slides that little ones can go on...most of them end up in DEEP water. The dig was nice...not the BEST aquarium ever...but good, and I'm glad we had a chance to go. We spent most of our time at the slides and dig...and didn't make it to the beach or other lagoons.
If your not wanting to spend any time at the pools, lagoons, slides or beach...you may just want to go to Atlantis on your own and explore the building...and some of the grounds (most of the grounds at Atlantis are off limits to non guests...and guarded at check points...so no sneaking in)
But over all we had a great time...DD6, DD11, DH and myself.