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I used to organize by type, but now I let general pokemon just inhabit all kinds of bullshit box space.
That being said, Box 1 is used for my team and any accessory Pokemon I might use (Flame Body Pokemon, special HM Pokemon, catching Pokemon, etc.), as well as any Pokemon that have yet to be properly sorted.
Box 2 is used for fully trained Pokemon, and so on until I don't have any more, at which point randomly caught Pokemon start appearing.
The final Box is used for Legendaries, and then moving backwards from there, Dittos, a Future Breeding Project Box, and then individual boxes for breeding projects where I store decent leftovers to give away (3 IV and below are wonder traded).
