The thing that jumped out at me when I started reading this post (a few minutes ago) was that in Red-24's picture on the first page, the overhead shot shows a difference in the rear quadrant of the saucer, between the bridge 'bulge' and the impulse engine. This would be the ridge that 'Ben' mentioned. I have just gotten started on a Klingon fleet with the fleet box, and they are individually bagged as mentioned (and the mini book does not have pics), so to keep the models straight until I learn them better, I copied the Klingon ship photos from the Mongoose site as a easy access reference sheet.
From there I plan to make desginator marks on the bases to keep them straight. That or different marking / paint jobs. Either way I expect to be a bit confused for the first few games.