I don't use FPSC, but if it can use transparencies on objects it shouldn't be a problem. I would suggest making a simple box, texturing it half red (or any color) and then leaving the other half empty(transparent) Load it in FPSC and see what happens!
If it doesn't work, then you don't need to waste your time doing transparencies while texturing your character. If it does work... Well, there ya go!
Not everyone in 3D chat will know the answer to this, but there are some pretty sharp folks over in the
FPSC Models and Media board that might be able to help!
Good luck!
There's something in this room that makes you can't speak well.