I was just in Nassau for the same excursion with group with NCL SKY cruise ship from Miami to Bahamas 2 weeks ago. The tour itself only took may be 1.5 hours, the guide walks you through the Atlantis Aquarium fast and you are released after that to roam around and do your own sightseeing and loop back. Of course, there's the beach area, which will cost you to upgrade/add-on to your Atlantis excursion ticket. Then there's the Aquaventure, huge water park, that will also cost you more. The island itself is beautiful just to walk around and there's Marina Village shops walking distance from the Paradise Island. If you're with your group and you took the shuttle, it's available on hourly basis to return to the ship. We were asked to return to the ship by no later than 4:00 p.m. Add time to get through the line for ID check to get through the port and then the line to get onboard the ship for ID check and package scanner. There's a plaza near the port that has more tourist trap shops from local variety crafts, Straw Market and then the brand name shops and jewelry stores. If you feel like catching a good Bahamian/Jamaican food for lunch (cash only), Pepper Pot Grill, walking distance from the port, between Market & George Street. Enjoy!