Jadehawk:
What you've been painting is the Diffuse Map. This is the basic texture that gives color to the mesh. There are other maps that get layered on in the game for different effects.
Shine maps affect the specular level and color of the texture. Here are the Harbinger maps for reference:
WEP-HARB.DDS
WEP-HARB-SHINE.DDS
The end result looks like this. Notice how the grain of the texture is enhanced.
You should add an alpha channel to your shine map to affect the level of Environment mapping. Everything opaque will have a mirror finish on it, good for cockpits and other chromed parts like those guns.
Glow maps are always rendered at full brightness regardless of the rest of the lighting. They are commonly used for lights, windows and the red Shivan glows. Here you can see the glowmaps active on the Hatshepsut.
Normal maps are (usually) generated from bump maps. Let me quote Herra:
The elevation map itself must be in shades of gray for the normal map plugin to work correctly as far as I know. So you will need to, at some point, de-saturate the colours in their own layers and then brighten or darken them according to their elevation (deeper = darker, higher = brighter).
Example might be in order before I confuse people more... 
This is of the workflow of the GTB Rhea normal mapping I did a few times ago... Of course, these are resized versions - the original work was done in 4096^2 resolution and the final normal map was 1024^2, but for everyone's sanity I'm using resized versions - they work just as well for showing what's going on.
Base diffuse map:
Stuff I want to have in the normal map. Blue is to mark seamlines, recesses and stuff like that, red is to mark stuff that extrudes upwards from the surroundings. The details are drawn on about five different layers instead of a single layer for ease of seeing what I'm doing (same reason as using bright colours that stand out from the base).
Same with a neutral gray background.
Greyscale version of the elevation map - red has become bright (elevated areas) and blue dark (recessed areas)
Finally, a normal map generated from the elevation map.
EDIT: The end result looks like this (click for full size):
To get the final normal map to actually work in FS2_Open shader system, read this thread here.
Also remember that this is just my preferred method of working with normal maps. Other most likely have their own methods of making them...
So in the end you would have TEXTURENAME, TEXTURENAME-shine, TEXTURENAME-glow, and TEXTURENAME-normal for each texture your fighter uses.
