Water Level Issues

Okay, so I used DarkLord's Terrain Heightmap tool to make terrain for my map, and it worked fine, but as you all probably know it raises and lowers the terrain, it doesn't make cliffs.

The terrain is all pretty steep because I intended for there to be lots of water around the landmasses. So, is there a way to made the lowered parts water without using cliffs through Zepir's WE or some other tool?

Starting the map with shallow water doesn't help, looks like all the water got lost in the process. Interesting...

Anyway.
Make sure Enforce water height limits is unchecked. Then place shallow or deep water on all those lowered parts where you want to have water in the end. Afterwards use the raise cliff tool on the water to get the terrain back to the normal height level.
Now just lower the terrain a bit to get water.