Not much to consider actually:
- make sure that the race you use in the game has the same ship-style you designed your custom ship with (e.g. Terran, Drengin ...)
- you have to start a new game before the ship is usable, just loading a previously saved game won't do (that's because all available ships are included in the savegame file)
- be aware that if you have attached functional components (weapons, defences, engines, modules etc.) to your custom ship you have to research those components in the game first before the ship becomes available
Hope this helps
