Okay, this is pretty easy. First, get a program capable of manipulating .dds files. In my experience, these are generally pretty expensive, so I suggest you get
the GIMP as it is free, and as far as I have seen, equally if not more powerful than Photoshop Elements. Then, get a plugin for the GIMP that allows you to work with .dds like the one found
here. Once you have made your texture and are ready to add an alpha layer, right click on your work surface or just go to LAYER at the top of your window, and go to mask, apply layer mask. Choose apply as alpha channel. Once you've done that, you are now editing the mask that will be your alpha. Edit this like any other layer, except it doesn't care about colors, it only takes the B/W value of your color and applies it to the mask. The darker it is, the more transparent it becomes. This transparency does not show up at all in your final texture. it is related to other values according to which texture you are changing. If you are editing DiffuseTextureFilname, the more transparent it is, the less shiny it is, and the reverse is obviously true; the more visible it is, the more shiny it is. My DiffuseTextures usually come out almost looking invisible when I'm done editing, but this does not affect visibility in game. If you are editing the SelfIlluminationFilename, the alpha creates a glowy effect where your texture is visible. this only really has any effect when bloom effects are active. The NormalTextureFilename does not use an alpha channel as far as I know. Once you have finished editing your alpha channel, follow the same route as before by either right clicking or going to the top bar, and go layer, mask, apply layer mask. Now go save as, and save as WhateverYouWantToCallIt.dds. It will bring up a prompt for saving as .dds's save it as a filetype with the option RGBA, probably the best is RGBA8. then just put it in your mod, and viola! textured ship.
Hope this helps, even if it is a bit long winded!
Ezraeil