Err, nono - that only works for 8bit PCX files - which you really shouldn't be using at all nowadays.
To get transparency happening in game now you will typically use the alpha channel of your ships main hull map - you put in a greyscale copy of your map where white represents the fully opaque parts and black is completely transparent. Once done you save it as a DDS with DXT5 compression. (Ie, don't use DXT1 (no alpha) or DXT3 (crappy alpha, no size benefit) compression)
Keep in mind though that FS does not yet handle transparency very well. It's got everything to do with what order FS finds and renders the various parts of the hull, but if you find you're getting weird transparency related errors, it'll more than likely mean you need to re-convert to fix it. I don't have time to explain the ins and outs of this stuff now sorry, but search for threads about making glass work on cockpits for more info.
Failing that I should have time to give more info in a couple of days.
