There are three ways of making things transparent.
Set the properties directly in AC3D if the whole object is transparent. (why you'd want to do this I don't know)
or.
Alpha layers which allow you to set 256 levels of transparency from none to completely see through. Make the image the same size as your original texture with the same name but with _a inserted. 256 colour greyscale.
Using truck.bmp as an example the alpha file would be called truck_a.bmp White will show the texture through completely, black will be completely transparent.
Or use the index system that HTC uses. The first colour in your palette of colours should be magenta R255 G1 B255. A .txt file then tells the program which colour on the texture is transparent. again using truck.bmp the txt file would just have the number 1 in it and would be called truck_a.txt
I've found alphas to be the most flexible. This is a lapsed project that I haven't looked at for a couple of months all done on a single 256x256 texture and a 256x256 alpha texture.
Gatso