Greetings from downunder,
It seems 2 issues are being asked here. Alpha channels and image mapping to polygon faces.
Muzo, do you have access to a 3D modeller that imports .x or .3ds files? If so import an fps .x model and unwrap the texture mapping, you will then see how the modeller has texture mapped/wrapped/baked his/her creation and to what methodology of madness he/she followed.
Swhale the first texture can be a 32 bit targa with alpha. Use the extra channel as a mask and remove the background. FPS will convert the tga into a dds on the fly when you test your level. The other DDS files in the sequence are for bump/height/normals mapping etc
International Digital Designer of Mystery