Go to colours - components - decompose - RGBA. Makre sure to keep both the original texture and the decomposed one open whilst editing though. Then either paste the teamcolour texture into the alpha layer or bucket-fill it black and go to colours - components - recompose, and the original texture will change. If you bucket-filled it black then the image will appear transparant, but as long as you save it in a format like dds then the other channels will still be preserved.

Thanks for the replies.  I found an easier way to do it though.  Here are the steps, first click on the Image drop down and click flatten Image.  This will get rid of the alpha channel that Gimp makes for you.  Then right click on the layer and click add layer mask; a window will pop up, then click black and click add.  That's it, then save it ass a dds and your good to go.  

If you have photoshop available in the Layers menu there is a tab called Channel which is where you can create your "Alpha Channel"

So essentially, create where you want to team colors to fall on the texture map for the ship (whichever file it may be) in a new layer above the "background" layer that is locked. Once you've got the basic coloring down, select the outside with your marquee tool or wand tool then right click to select the "inverse selection" and then right click again and "save selection" then a menu will pop up and ask you to name and save it... Save as Alpha channel... this might also help some with editing some of the menu graphical files available in the textures folder for modders... I love my Adobe Photoshop CS3