Unless Atlantis has changed it policy(again) you must be a registered guest of the hotel to have access to certain areas of the hotel, the private beach and waterslide area.
You can go to the casino, tour the Dig and wander around the public areas (main lobby, restaurants, shop area) without being a guest.
I do not know what the ships excursion gives you access to. Ask your travel agent to find out for you.
There is a large aquarium there. I was told it's the World's largest. It's a guided tour but the pace was very fast (at least for me). After the tour you can go back and see the aquarium again. There's a mall and casino in the hotel. The hotel also has a mini water park.