My shipset was coded up for me, but from what I understand you need an objgfxcfg file for that ship in your game files /Designs/Startup folder. And it needs to be inserted into the compressed objgfxcfg folder in there as well. It may be that it only needs to be in the compressed folder.
This makes it actually a mod to code and not just a mod directory entry. So you have to be ready to put it back after each update or reinstall. Kind of a pain, but worth it for pretty ships.