When you make a map, right click on it in the tool bar to set it for a location. Really, you can find how to use a map on the Wiki.
Anyways, I will agree that I dislike the whole grid-based map system. I preferred having the map centered on the crafting location and originally expected the maps to be centered on where you activated them when I first heard of the change. Oh well, looks like it's something I'll have to live with.