Nevermind, it appears as though everything works, the small GIMP channel views, however, do not get updated for transparent colours. I should've done a bit more testing before creating this post and making myself into even more of a clown   oh well, live and learn.

Yes, I never did figure that out. I use gimp for everything now but the final step.

In Gimp, I save the final cl as uncompressed TGA, I also have 2 TGAs pure black, 1 512x512, 1 1024x1024, I open the new cl in an old photoshop and create an new channel called Alpha1, drag the black tga onto PS, CTRL+a, CTRL+c, go back to cl'c alpha1, ctrl+a, ctrl+v, save as DDS.

SOA2 does not use team colours, so all black, but if I open the cl.dds the alpha channel is gone because it is all black, but it still works as it should. That is why some reccommend 1 px of white in a corner somewhere.

If you don't have access to PS, zip me a folder and I can whip up a few for you in a few minutes. just specify if you want 1px white or solid, or your seperate team colour tga.

I guess mt biggest problem is editing the RGB color channels of my texture when the Alpha has to stay transparent in order to prevent the entire texture from being team color. In the meantime I'm fumbling around with stock textures to try and figure out how to do what I want.

MyFist0, do you make your textures in GIMP simply as RGB then go into photoshop and add the all black alpha channel?

Also, thanks so far guys, I'm sure I'll have a eureka moment eventually and feel real dumb for months.

http://soase.x90x.net/?i=xsi/Tutorials/Texturing.html

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Guide to Edit SoaSE Textures by Major Stress