I think he is asking more along the lines of texturing the model.... All I know if true black or #000000 is the only transparent color he can use when texturing...
But I am not 100% on this because I would like to do diffent depths of transparency myself on one of my projects.. mailny for a store wall I am working on.... part glass and part brick
But if your just looking to place a window on your map then bdgbdg is correct choose it from your segments vs your entity folder if your attending to get full use of the window the way it was supposed to preform on the map...
Have you downloaded your CLiPs today.