I prefer to spend more time and set up individual auto-pulls to keep like items in individual sets of boxes. Like I've got two boxes for hull pieces. One does normal hulls, one does crystal hulls and doors. I have a box for lighting and glowie crystals, and above that a box for motherboards/circuits/ingots. Boxes for weapons and their computers, boxes for support systems, etc etc etc.
Takes for bloody ever to set up, but once its up and running its very, very nice.