Thanks for all this great info guys. Watching videos and trying different things with seed and map generation the last week, and through a lot of trial and error making good progress. Going to try this file now. Also having issues with certain areas filling up with road tiles in paint.net when removing/modifying roads. Going to try paint black behind as suggested. I let you know how it works.
One thing, should I be saving to 32 bit? Clean files says 32bit, but i noticed some files were lower bitrate after i modified and saved them. I did have the save auto detecting the file, which i just hard set to 32 bit, hope that helps. Also, the files seem to be getting smaller as I modify them. Granted, I'm not removing large areas of the roadmap, Ive been adding roads and shuffling buildings around. Any ideas?
Edit - Figured it out d'oh. Painted empty space in with solid black, bingo.