uhm.... you would get better answers if you would ask at the modeling section lol.
You can alpha map with transparencity in photoshop with the PSD or TGA file (possibly GIF aswell) ,what matter of the programm you use.
or use the B&W basic technique... white is whats transparent and black is what you see, you can do grey so it would be lik 50-50
forgot what what is, i gues Bolteh is right xD