-bye typing(primary typing eg. Charizard is fire/flying, so he would go in that box)
-your training Pokemon in one box, breeding in another, and your goto wifi team in your battle box, the other reserve teams can be put in a box
-don't organize your pc, as by memory you may be able to find things straight up
-Legends in one box, with a combination of the other options for non legends
Those are some ways I've done it.