Depending on which version you wish to play on the GalCiv2 Ultimate:
DL folder: '...\My Documents\My Games\GalCiv2\ships'
DA folder: '...\My Documents\My Games\GC2DarkAvatar\ships'
TA folder: '...\My Documents\My Games\GC2TwilightArnor\ships'
I tested them on TA, and they work. Not sure about DL or DA as I don't really play those versions that much.