Not an unreasonable request at all. It's simple to do an underwater glass dome in Omen.
1) Fill the black world with water
2) Select brush, set the size to X and material to GLASS and mode to 3D Circular
3) Find the center of the map at the lowest point (highest Y value)
4) Click once
5) Set the size to X-2 and material to AIR
6) Click in the same spot
7) Do as you wish now
Remember, you can use 2D flood fill to lay some ground.