If you have the original model, just rotate it in a modelling program so it's right side up--the game uses it exactly as it is there, AFAIK, so if it's upside down then it was like that originally, or something went weird in the .x conversion process.
If you can't edit the model, then the simplest thing is to just add it as jewelry instead, and stick it on a brick-hull or a blank (using KHSM), then you can rotate it to the right orientation using the normal options in the ship designer.
