I might be able to help a little. I took a RAW model (The aion) and then used paint object to cover the model with a basic hull coating (teh defualt texture). I saved and then open the model in 3dexploration and now it had a texture slot.
I filled that slot with a predetermined texture for Main Hull.
saved the model, and then reopened with TS3.2
Chose Paint Face and started painting polys I wanted to be the same (ie a cockpit, weapon ports, hull trim, etc)
For each piece I did all the same parts at same time (lots of undo hits as I messed up and slipped a LOT). Before working on a new texture I saved and then applied the new texture in the new slot that appears in 3d exploration.
I did this about 9 times over for the fighter. For a cap ship it would be a lot more...
I hope that helps you a little as that's how I had to do it. I barely know how to use 3.2 to port a ship in the game...
If there is a better way hopefully one of the old timers will chime in or you could go to the Calligari forums.
L8tr!