When you open it in Gimp, find your channels and add an alpha channel. I think it's just right clicking in the channels' window will show the option. Look up the help info on channels if I'm wrong...
My preferred way to do the textures is to use the exported unwrap as a layer with the base/background layer set at 100% transparency. Since the unwrap is a layer above, I just have to erase (or adjust the amount of alpha) portions of the actual texture. When exporting back to TGA - which doesn't have layers - I don't remember what the difference between "flatten image" and the other option is. Either one works, just remember to use the "Save a copy" and not "save" because if you save the actual file as a TGA you'll lose your layers - not good if you weren't done editing it.
