I think Hoooneylynn has some horror stories to tell when she tried using sand in her tank. Personally, I wouldn't try it since any sand that is fine enough to not be a danger to the turtles will most likely be easily stirred up by the turtle's movements and make the water cloudy.
You are also right about having any kind of dirt/sand nesting area making the tank water dirty. You may want to make a separate nesting container that can be attached to the main turtle enclosure only when needed. You could incorporate some kind of shallow water tray between the nesting container and the main enclosure so the turtles can wipe their feet before going back in the water.
I can't wait to see your finished project!

Sounds like fun!