If having the thread unspool the wrong way is a problem, one extra step that should correct that would be to wind another bobbin from the one you just wound. It's pretty quick to do, and would solve the problem - just so you don't forget which bobbin is wound which way. I would use a Sharpie and write "TOP" on it just before winding or would have to be careful not to get ink near the holes and onto the thread. . Permanent ink can be removed from hard surfaces using rubbing alcohol.