Early in the game, I don't rename anything and mostly work out of Box 1. I put duplicates in the last box - the first one to the left from Box 1 - but that's about it. As I get more stuff though, I start expanding. I divide the pokemon I'm going to actually use by how useful or trained or evolved they are. Box 1 becomes "First" and is for the first string - the ones I use a lot and depend on. By late in the game, they're pretty much all fully EV trained final evolutions. Then going to the right, it goes down through some arrangement of second string stuff, stuff I'm planning on using that needs to be trained or leveled, stuff I think I might use, stuff I think I won't use but haven't given up on yet, new stuff I haven't decided on yet and stuff I know I'm not going to use. I don't have any set system for that - it depends on how many of each category I end up with. They all end up with prosaic descriptive names like "Likely" or "Doubtful." And going from the First box left I go from Dupes (mostly stuff I plan on trading) through stuff I plan on breeding, stuff I've already bred (mostly parents with good natures and/or egg moves) and babies. If necessary, I have boxes somewhere in the middle for shinies, legendaries, nice stuff that doesn't really fit in anywhere else, HM slaves and anything game-specific, like Unowns. And in games where I do a lot of breeding, I generally end up with a box of Dittos. And starting with White, I've been adding a box in the middle (with the beach background) called Miami - that's for pokemon who served me well, but are now retired because they got replaced, generally by the same thing with a better nature or some egg move(s).