Wow Sue! How exciting that you were able to see Hannah Montana. How was the concert? I'm sure it was great!
My understanding of the connection between Atlantis and Comfort is that they are owned together. So when you get a room at Comfort you are allowed to use the facilities at both hotels. When you check in at Comfort they give you a wristband for each person in the party and that allows you to go between both hotels to use the facilities including the aquapark, the aquarium, etc. It's much more economical than Disney's excursion for the same thing, that's why so many DISers have done it this way, saves a lot of $$.
Hope that helps! There are also several threads on the main cruise line forum of people talking about this very thing. Unfortunately the search engine never works so you have to go page by page usually to gather up the info. But I think that's pretty much the deal.