Go to the "Terrain" tab (where you paint grass, coral,snow and such) and select "Deep Ocean" and paint over the areas that you want to not show up and save that.
Then open your terrains .oba file again.
Then create a new clip board map and every thing should be good to go.
Home for lunch, but that should solve your problem.
midi
Edit: Also before anyone jumps in and suggests editing the gndtype.bmp file, all tho it can be done that way.
I am putting that as well as editing the waterd.bmp files in another tutorial.
so for now stick with the above instructions first and you should be safe from breaking anything..LOL
midi