Is it something I'd be able to implement with Milkshape for the Halo model I converted for a bit of variety, for example? If so, how is it done, and would I be limited to two different skins like the TSA soldiers?

I dont know about how many skins are allowed but put this in your .qc file
just replace the text with your texture.

$texturegroup skinfamilies
{
{ "your_texture_here.bmp" }
{ "your_other_texture_here.bmp" }
}