Alpha maps and team colours

I have some experience in skinning and i have recently started to get into skinning in warcraft 3. However I have run into a problem. It seems you can use alpha maps to not only show transparancy but also use them to show team colours. The problem I have is I dont know how to set which is the transparancy part of the alpha map and which is the team colour part. Can any body tell me how to do this.

cheers

Red Fox