We just did this on Tuesday and hated it! We booked through Disney. They had us meet at D-Lounge at 11:15am and then we headed out to the bus. Nice, air-conditioned bus and it's a quick ride. Atlantis is beautiful. However, we had the worst tour guide. She was just awful, slow, monotone with very outdated jokes. Some of her comments made zero sense with what was going on at all. The tour was way too long and drawn out for my kids. Honestly, we wished that we would have stayed on the boat.
Overall, I loved the comfort of booking through Disney for their transportation to Atlantis but would have rather explored on our own instead of a tour. It would have been much more enjoyable for us that way. I felt it would have been rude to leave the tour, but I really wished that we would have. Disney makes it easy to get there and was worth the extra money. If you decided to break away from the tour, grab a map! The aquariums are a little spread out and might be tricky to find on your own. Also, make sure everyone leaves their wristbands on and visible. Their security is very tight about what areas you can access. Kids wanted to see the waterparks, but you can't get anywhere near it without the proper band.