I didn't modify the map generated by the TE at all.
I used Gimp, coupled with a program I wrote that will let me convert a greyscale bitmap to a indexed color bmp using the color palette of my choice, which I ran against *(an appropriately sized version of) the heightmap for my terrain to make a color terrain map to use as the graphic for my in-game map.
Then, in Gimp, I layered on markers for fields, bridges, and rivers, as well as the grid and the grid cell numbers, and saved the composite to a indexed bitmap.
I'm not quite sold on my current color scheme for the terrain map, and had intended to refine the color choices before submission so they don't look quite so "harsh", but generally am sastisfied with the process if not yet the results.
Guy
*(If you are making a 256 mile map, you have to cut out the center of the heightmap, scale it by 2, and use that, since the ingame map is a 1024x1024 indexed bmp).