Personally I just make my ships by hand now, without using a ship editor. It's a pain in the neck BUT you get a lot more precise understanding of what's going on where, and can also set up some cool stuffs like split room designs etc, which I don't think any of the editors allows.
That being said, if you do want to use an editor, I would highly recommend superluminal:
viewtopic.php?f=12&t=11251 as it is far better (in my opinion, no offence to anyone) to use than any of the others currently out there.
At the end of the day though, the most important thing is to have a solid idea for a ship. If you have a great concept, and work at it, you will get it done in the end, one way or another.