Hey there m8.
Actually your Alpha will still work as long as the texture you are working on has a _t.bmp for it's name. The _t denotes to FS that it is a reflective texture,all you need to do is paint your Alpha channel window areas with a 230/230/230 or lower grey value and it will reflect. As for window color,I prefer a bluish-grey for the coloration. It all is dependent as well if the windows have a transparent material applied too them on the original model.
Hope this helps you m8
Cheers
Randy