Thanks for answers guys! I will look over my collection and the way that is more prevalent is the only that I will use. I get OCD about organizing files sometimes. I spent 5 hours last night just going over covers and choosing the best one and trying to make all the covers from the same collections or the same editions when it comes to the same author. I think I spend more time playing with it than reading!
Another question I had was that if when you do a conversion you can set it so it erases the previous file.