Gimp user...
Save the color scheme you want to edit with Gimp, in the RF sim. Go to AIRCRAFT, then click on SAVE COLOR SCHEME AS, then rename the CS to your choice. Open the CS in the sim, to create a DDS file. After this, look under your RF directory for COLOR SCHEMES, open the folder. look for the new name, and open the TGA file with the GIMP program.
change the colors you want then go FILE, SAVE AS, REPLACE, then uncheck both boxes and press SAVE. Go to RF, and click on your CS name in the sim. if you do this right, you should see the change after the DDS changes.
I created the Gimp Users Guide To Color Schemes, to compliment this thread. You will find helpful hints and tips to make your CS the best it can be.