OK HERE IS THE BEST WAY TO ORGANIZE YOUR BOXES AND KEEP TRACK OF POKEMON YOU HAVE.
First name your boxes by regions
Kanto 1 , Kanto 2, Kanto 3
Jhoto 1, Jhoto 2, Jhoto 3
Hoenn 1,Hoenn 2, Hoenn 3
Sinnoh 1, Sinnoh 2, Sinnoh 3
Usually each region needs three boxes. After you do this PUT ALL THE POKEMON IN THEIR POKEDEX NIMBER ORDER. If you don't have a pokemon, there will be an empty space. Yes, it takes time...but it ensures that you have all the pokemon from every region and tells you what pokemon you need.
SO in Kanto starting from Venasaur...ending at Mew. You don't have to have Bulbasaur, Ivysaur..Just have the last evolution, do that with all pokemon unless they don't evolve ofcourse. After you are finished you will still have 4 boxes left...DO WHAT EVER YOU LIKE WITH THAT.
:16: