It says in the manual "The easiest way to create a working map file is to use the map editor in Dominions 3. Load in the map you have drawn and click in all borders and terrains.", however nothing happens when I click on the map, and there's no "all borders and terrains" button. So, how does it work exactly?
You need to draw the map image, including any borders if you want the borders visible. You must also include a single white (255, 255, 255) pixel in the center of each province.
You then load that into the map editor and assign neighboring provinces and terrain for each province.
Also with provinces I advise providing extra room on the top left for the borders of all provinces because this is where the image for victory point crowns appear. If there's not enough room a victory point crown image will appear in another province and cause possible confusion for new gamers.