Don't worry, you will LOVE Atlantis. We visited a few years back. Your boys will love the torrid river, which is a million times more fun than any lazy river around this area, Wisconsin Dells included. My family was on that every day! Awesome fun!!
We did a dolphin encounter excursion that was not through the Atlantis resort because this was much cheaper, and it was lovely. Sorry I can't remember the name of the outfit, but it was an easy walk out of the resort the little boat cruise area.
Be sure to get to the pools/waterpark early each day to get a chair. And also know they close at 5 or 6, so you can't do evening waterpark activities.
I will warn you it is very difficult to go off-site to eat when you are at Altantis without taking a taxi or a significant hike. We could not do it at all, though our girls were much younger than your kids. The bridge to Paradise Island isn't exactly pedestrian friendly. The food at the resort is heinously expensive at ALL the restaurants, I'm sorry to say. BUT it is so GOOD. Loved the sea bass at the restaurant in the main lobby that has such wonderful views of "The Dig" aquarium. So I would advise you just to accept the fact that you will pay a lot more for food than a typical vacation, but just decide in advance to be OK with it and enjoy.
We stayed at the Royal Towers. If you take a little walk through the casino, you can find a little boardwalk area that has some less expensive places, Johnny Rockets, a pizza place, ice cream, etc. It's a beautiful stroll with shops and great views of incredible yachts too.
Have fun, I'm envious!