You can take a taxi or a ferry. We took a ferry from just outside the port. We paid inside the shops, $6.00 pp round trip. The ferry takes about 10 minutes or so. It's a beautiful ride but as is in the Bahamas, the guy who talks about the islands will expect a tip. As for Atlantis, we walked around the shops and casino but could not get near the pool or beach are. Someone stands at the top of the stairs/walkway to check if you're a guest. A short walk from the Atlantis is Cabbage beach. This was nice.
We got a mini van, which I think was about $8 each. The kids wanted to head straight to the beach, so we were dropped at a public entrance to beach just up from Atlantis. Beach was nice but ocean was very rough, kids couldn't go in, which was a shame. after a couples of hours digging castle and holes we walk back down to front entrance of Atlantis. Walked around the Aquarium which was really good and acroos bridges with hundreds of rays swimming under, beautiful. This was free. Their fake Caribean beach was very tempting (after the rough ocean avaliable) but we were told £150 for two adults and two kids, for the wrist bands and towels which would intitle you to use pools and slides. as we had to be back on ship at 1.00 it wasn't worth the money. The guards will let you through to the beach from Atlantis but they will stop you if to try and walk to see the Mayan waterfall area.
If we done it again, we would head for Cable Beach (more Caribbean) and get a day pass at say Holiday Inn.
If you just go and walk around yourself, you won't need that much time, but I'd suggest taking the tour. The "dig", aquarium is something to see and I don't think they let you through there unless you take the tour. If you take the tour thats at least an hour.
The Atlantis isn't huge, its just basically a large-scale hotel (think Las Vegas big) and some stuff to do & see there. The shops inside the Atlantis are expensive & tailored to the rich. You aren't going to buy expensive clothes $200 & up. There's a nice patio overlooking the lagoon where you can get some lunch or walk around & look at the sharks & such in the underwater viewing area.
Other than the beach or the casino, there's not much there. We stayed there a few years ago when the Atlantis was just about to open. It's expensive to eat, you get better food prices on the other side of the bridge.
Cool to walk around, probably take you an hour or so at tops depending on what you want to do.