That's the way I did it too - until I found how to use the colorization tools of the skin editor! Try all the buttons under the skin map window!
Select one of the color windows, click the bigger button near them to choose your preferred color, paint with "Fill Selected" for instance, that's the fastest way to mark certain triangles.
Then export the resulting picture as bmp or pcx, and edit it in any grafic program that you like!