for starting read this: https://forums.sinsofasolarempire.com/346180
after that find your "RaceLogos.tga" in your game's directory/textures (as you can see it's .tga, not dds.)
make your back-up file. open the racelogos.tga. in he right panel on the second tab there are the colors. don't forget to make the alpa channels for them, and the mini-logos down below!
i made my racelogos with photoshop, so I can't help much more. Good luck in gimp. 
