>>26713782Start by renaming your bank boxes: 1-30, 31-60, 61-90 etc.T hen, just go through your accumulated Pokemon and sort them into the correct box / slot. If you have bank, you can search by national pokedex number, and that's a big help. That will give you the framework necessary to at least start.
I subdivided my missing pokemon by generation:. I was missing 15 pokemon from gen 1, 30 from gen 2 and so on. Then I just picked a game and started hunting for all the pokemon I could find in it that were on my list. It lead to me having some really memorable teams, I tell you what. I never would have used many of my pokemon if I hadn't needed their evolved forms. Also, it's rough boxing up a fully evolved starter, but even harder boxing the 2nd stage evolution because you need that Grotile for pokedex completion.