First of all, I think Stingray City is definitely worth it. If you are scheduled for late seating dining you should have no trouble doing all that you want to do. The ferries that transport you to Stingray City are located at the Paradise Island ferry dock, within walking distance of Atlantis. Depending on when you are scheduled for Stingray City, you can easily check out Atlantis either before or after. If you are pressed for time, there is a smaller version of the Straw Market on the corner between the ferry dock and Atlantis on Paradise Island and you would certainly have time to do some shopping there.