PokéBase - Pokémon Q&A
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-bye typing(primary typing eg. Charizard is fire/flying, so he would go in that box)
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-your training Pokemon in one box, breeding in another, and your goto wifi team in your battle box, the other reserve teams can be put in a box
-don't organize your pc, as by memory you may be able to find things straight up
-Legends in one box, with a combination of the other options for non legends
Those are some ways I've done it.

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I always put the Pokemon I use in the first boxes and the other Pokemon pokedex,breeding etc. In the other boxes. You can move multiple Pokemon at once by using the green button at the top right of your touchscreen when you click 'organise boxes'. Then select a row or more by using your d-pad.

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Thanks!