You have 3 files in the programs files you have to edit, and 3 files in the resources folder you need to edit.
If however you wish to add a new ship, its a little more complex. Load your game and as long as the ship had the ship(s) had the same name(s) as the ones you replaced the game will be fine and the ships will be generated as normal. Do the same for the vicotry and thats it. Now open resources/textures/ships and open the ship folder for consitition Hull1, 2 and 3 need the files deleteing and the new ones adding in there place.
If the ships from the POTC build mod use the exact same names as the ones in GOF then its very easy to do, just go to your resources/models/ships and delete all the GM files for the consition and victory and put the ones from the POTC build mod in and add 1 at the end of the ships name for each of the GM files ie, consitition1, victory1 etc etc.
