Right, photoshop. Bear with me as Im doing this from memory, as I dont have Photoshop here,
and yours may be a different version. There may be some differences.
1> Open your texture in photoshop. (Original format un-important)
2> Use magic select tool with a color-range of 1(one), contiguous to select the UNUSED space
between your texture parts. All of it if possible, if its a bit broken up.
[dont de-select this mask till I say so,
its important, we'll need it later]
2a> Optional - if you can find it, there is an option under the selection(?) menu called "Contract".
Its used to shrink the selection by xx number of pixels. Contract by 5 or so pixels.
3> Find the panel that normally shows the different layers on the image. It has a tab called "Channels".
Hit that and somewhere on this panel is a way to add new channels. Add one. It should call itself "Alpha 1".
Leave everything at default and just hit OK. You should now have a single, uniform color displayed.
4> Choose the Greyscale 0-100 pallet (happens automatic I think) and set the current color to WHITE (0%?)
5> Go to the selection menu and choose Invert, to invert our funky selection mask.
6> Fill in all our texture areas with our dead white till they are all done.
7> Now you can dump our selection mask. Basically All Done.
8> Now you can go through these Texture parts and give then different alpha levels.
REMEMBER the numbers 3dGS will see is the opposite of the 0-100 scale here in photoshop.
What you set to 10% here will be AlphaValue=90 in 3DGS.
ALSO REMEMBER you will need to make the RGB channel visible (on the channels panel) before you save.
When you save, TGA (32bit) is the best for this job. BMP's just get too big. And make sure the "Alpha Channels" box IS ticked.
That should get you started. Any questions, just ask.