Yeah unfortunately it really isn't as easy. There are no guides for that and the video tutorial conviniently skips the whole water level heighmap creation all together. Sure biomes and cities and zoning are there but water levels... Nah. So, having fought over and over with this by myself with no help, it simply will not work. I create heightmap (anykind, any method), paint black areas (anywhere, nowhere), save correct formats and sizes and... The whole water levels gets screwed, putting water where it wasn't supposed to be. Or just not putting water at all.
It most definately is not a simple 10min thing to add to my hobbies. It's clear that some of you are simply that much better and things are very easy for you. Good for you, just don't expect everyone to be on that same level.
I'm giving up and it's not for the lack of effort. Sorry for being salty but i really could have used this time for other things.
Excluding the water editing, this tool is still very good and kudos for that.