What I would recommend for the flooding effect is to put in the selected area using coordinates, have the value set to 0, and have it on replace mode to replace air. It should look something like this:
/fill <x> <y> <z> <x2> <y2> <z2> minecraft:flowing_water 0 replace air
For cloning the level in, you would just have to use multiple command blocks that clone the area from different places.
