I use Photoshop but I guess other paint packages are similar...
Make your texture image & save it as a 32-bit RGB .TGA file
In your paint package there should be a way to see the "channels" ie:
Red, Green & Blue... There'll be another channel there too, this is the Alpha Channel & will probably be blank.
Make a greyscale image to determine the opaque & transparent areas & paste it into your alpha channel.
When you re-save it the image file will then contain transparency info hidden in the alpha channel.
Be sure to change the object's transparency setting in the properties editor in FSPC otherwise the transparency info will be ignored.
Hope this helps