Here's a map that my DH did that might help. BTW you get a copy of this map when you get your wristband. You carry it with you and it makes it easy to find your way around.
A is where the taxi lets you off.
B is where you get the wrist bands.
C - H are things like the slides etc. that you can only get access to with a room key
X shows some of wildlife lagoons.
The area shaded in red shows the Dig areas. S marks the start of it. It starts under the main lobby and winds underneath the hotel. You can see some of it from the lobby area. You walk downstairs and to get into the Dig area you just show your wristband. Then you take a walk outside and you join the second part for the predeator tank under the large round building near letter E.
It is a lot of walking if you want to take in all the outside stuff as well. We walk all around out near the beach and everything. There are lots of little lagoons that have stingrays, sharks, etc. There is also a great rope bridge that I think the kids will like. It is a lot of walking but if you do it on your own you can do as much or as little as you want.
I agree with Cruisin'Kroezes that the water taxis look scary. I took one in Nassau years ago (before Atlantis) and never want to take another one!
Any other questions please don't hesitate to ask.