Pangeas,
Your problem is white pixels (RGB 255,255,255).
Dominions knows where provinces are by these white pixels. To use white in your maps, use something like RGB 254,255,255. To the human eye it will still look white.
Once you have all of the pure white switched to off white, you can draw a single white pixel wherever you would like a province. Then the flags will only appear on these locations. Province borders must be drawn manually. You define neighbors in the map editor and terrain for individual provinces. I think that once you have your pixel problem straightened out and play around in the editor you will start to see how it works.
If you still have specific problems, feel free to ask in the
Scenarios, Maps and Mods forum forum.
Oh, and welcome to the community! We can always use more maps.
