Welcome back Linet! I'm happy to hear you're getting ready to book some exciting Port Adventures!
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Discover Atlantis Port Adventure is a really great way to see that amazing resort, and letting Disney plan the adventure ensures that they take care of all the details. Your Port Adventure will meet either on the ship or just off the ship on the docks to take you off to Atlantis. You'll have a narrated drive to show you some of Nassau on your way to the resort. Once there you can enjoy a 45-minute guided tour, and then the rest of the time there is on your own to explore. Since there will be shuttles leaving the resort heading back to the port area every half hour from 1:00 - 5:00 p.m., you can choose to leave at your leisure.
Don't worry about missing too much back on the ship. There will be many opportunities to take part in the events onboard, but only one chance to explore Atlantis. That being said, if you do head back early, you will be able to take advantage of some of the normally crowded areas of the ship, like the pools, with little crowds, so that is certainly an advantage of getting back on the ship early!
Have a wonderful cruise, Linet! Please stop back with any other questions!