In my setting's continent map I have a large, sandy desert that is the result of a previous mageo-technical war between the ancestors of mankind and <spoiler omitted>. The strip was the center of human civilization on the planet at the time and it was heavily bombed from orbit. The area is still polluted with the fallout - a substance tentatively called voidstone, which acts as a mana sink and has made the place somewhat inimical to life and has some very bad effects on magic. It is, as you might expect, one of my centers of psionic activity. It's also the home to a nomadic Chinese-like culture.

Now, I knew I wanted some of this in there when I started making the regional map but the unlikely placement of the thing comes almost purely from messing around with the map in the early stages and laying a "climate gradient" over the whole thing. I saw it and thought, "that's perfect" for a number of reasons and then fleshed out the story a bit more.

So, for me I think it'll generally be a bit of an iterative process. I didn't *just* use story to cover for a botch in mapping...I used a happy accident to develop my story further.
M