My family went last year over July 4th. We enjoyed it very much. When you first get off the boat you take a taxi/open air truck to the dock where a boat takes you out to the location. It is about a 10 minute ride and it is fun to see the Magic and the sights from the boat.
Once you get to the location you will see the Atlantis docked and you will dock right next to it so in an orderly fashion you will wait for the people who may be coming off the Atlantis before you get on and then you board.
I found some photos that I took from last year and posted them below. The photos are in order which would be the sub from above, the passengers loading on the sub, a photo of a small shark through the porthole, and lastly a photo looking forward of the tour guide/pilot who takes you to an approximate depth of 100 feet where you can see some cool fish.
Please keep in mind that luck plays a big part in what you see, some trips have better results (more fish to look at) than others.
Have fun,
Jeff