I can only tell you what we have always done and has worked out well.
At the end of the dock you'll find taxi (land) drivers to take you to Atlantis. The price is $4.00pp and $l.00 for toll on the way over which you can share with other passengers (no toll coming back). Have always found these drivers very pleasant and eager to answer your questions. Your taxi may be a limo or a van and have other passengers with you. The driver will walk with all of you through Festival Place and the car will be outside that area. When through at Atlantis, you'll find a taxi right outside the door to take you back to the ship.
The water taxi used to be right at the end of the dock also but has now moved further away down toward the Straw Market area. We took a water taxi on our very first cruise but that was on our own and not thru Disney. I would recommend the land taxi as it is much quicker.
Have a wonderful time.