Took this tour a few years back and we all enjoyed it. You meet on the ship in a designated area and go as a group to the waiting bus on the dock. Yes, tour of the city on the way over and your tour guide will also tell you about Atlantis before going underground to the aquarium, again as a group. It's quite a place and we found it most interesting.
Following the aquarium we were free to roam the grounds on our own as we wished. Don't think that's included nowadays (unless you pay extra there) but you certainly can wander around the hotel lobby and shops as well as the casino. Can't say anything about the casino as I've only walked through it. Catch your ride back to the ship, whenever you're ready, at the same entrance you were left off. The ship has a set time to depart from the port so make sure you know the "all aboard" time before you leave.
