I have one box for trophies, one box for starter pokemon (all 12 original starters plus the electric pseudo-starters [Pikachu, Mareep, Elektrike, Pachirisu, Shinx, etc.]), one box for my team and pokemon I plan to do something with in the near future, one box for Eevee and all its forms, one box for the masses of duplicate pokemon I get from the pokewalker, and one box for Unown. The rest of the boxes are for pokemon I just catch for the sake of filling my pokedex.