The folder that your textures are in match the ship you are textureing.
In other words dont use textures from folder GBDD on ship from folder GHDD it wont show up in game.
Took me a while to figure out why my textures were not showing up on my Heavy Destroyer, it was because I used the textures from my Battle Destroyer folder, instead of the Heavy Destroyer folder.
Oh well, live and learn I guess.