I'm not sure if this is the solution to your problem (In fact, I don't quite understand what you mean with this: "but the map is a smaller strip not covering the main window; it is unworkable.") But I used to have a problem with the mission editor not using the full screen. It was always just a bit too small, most noticeable when there is a properties window open. I always had to shift it up to be able to reach the cancel or ok button. Well, somebody made an edit on the mission editor program and this worked for me:
http://www.mediafire.com/?emolujghydq