I run into the same problem all the time. I've learned to use a Sharpie to mark the frame facing me when I open up the drive before I take anything else apart. I also use a silver Sharpie to mark the bearings on the worm gear to make sure I put it back together the same way I take it apart. Lacking that, there should be a white mark on the side of one of the magnets, too. If I remember correctly, that goes on the side facing away from you when you're reassembling.
Worst case, put it back together and run it with another DC engine. If they both run in the same direction, you win. If not, then you know what you have to do!
Lee