What is the fastest way to tear my custom map down to the lowest point of the map?
Also, how to add water to my maps?

Water = lowest level, you just need to paint the floor blue to make it look like water. The level above water is indestructable, and all the other blocks are normal.
Someone here probably has an empty template they can share..

(and btw, this probably belongs in the 'Maps/Mods' forum)