you should use DXT 5 and generate mipmaps!
for the alpha: duplicate the alpha channel to a new channel, flatten your skin before exporting to dds and then apply a layer mask using the duplicated alpha channel then apply the layer mask to your single layer...after that you can export to DXT5 and you should have a window texture with working alpha don't try anything else as you won't get satisfying results
for the skins you should use DXT1 and generate mipmaps too
(for explanation: the mipmaps make the texture smoother on distances...without the textures look sharp and edgy even with full AA etc.)
Ah right cool will give it a try this weekend as well. I normally save the mipmaps for the car skins but not the window files