I get what you're trying to do here, and I like the basic concept. I think, at times, I do the same thing, I just keep it in my head though. As for creating a "real" map based on the areas defined by your relational map, might I suggest RobA's Using-gimp-create-artistic-regional-rpg-map tutorial. Even if you aren't using gimp, there are several good concepts there that might help you get a more natural/shakier look to the various sub-regions of your "real" map.

GW