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How do you organize your pokemon boxes?

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I usually have a box for Kanto pokemon, another for Johto and so on for the ones that aren't trained yet, and then I have one for bred pokemon and another for the ones above level 50.
 
I orginize mine by EVd uber, EVd OU, EVd UU, EVd NU, IVd, and junk pokemon :)
 
Well, I never really 'collect' Pokemon for the Pokedex information, so by end game, I normally only have 5-6 pokemon in a box, so I keep them all in box one.
 
At first, I just had a box for my teams, breeding, eggs, and trading. But once I found PC, I started to reorganize my boxes into:

- Team
- Shiny/Legendary
- Breed
- Eggs (x2)
- "Garbage" (x4)
- Keepers (Pokemon that need to be trained)
- Chain (Umbreon and Espeons with different natures)
 
- Chain (Umbreon and Espeons with different natures)

I think you mentioned that in my pokemon training thread.

Right now I'm naming and changing the wallpapers of my boxes to number categorize my pokemon. So my first box would be Bulbasaur, Ivysaur, Venusaur, Charmander, Charmeleon, Charizards, Squirtle, Wartortle, Blastios and so on.
 
I never organise, just put the inside!
 
I organize them from the most important to the least important, so that means all the Pokémon I plan on using are in the first box while the rest just stay back in the others.
 
I only organize when I have time and when I feel like it.
 
When it comes to organizing my boxes in every game I get very very OCD. Each box is one type, though usually I put ground and rock together and grass and bug together because they match.

The type boxes are in alphabetical order.
Inside the boxes the pokemon are placed in alphabetical order also. The only thing that breaks that pattern is when it comes to the evolution line.

One box is solely used for legendary pokemon, while the last boxes are used for eggs, multis, shinies, and HM slaves. They are also put into alphabetical order. The legendaries however are put in order from their appearance in the games in general.. like the bird trio would be before the legendary beast trio.
 
In no particular order other than guaranteed order...

#1: UNOWN (one of each of the 28, and Baltoy & Claydol)
#2: DESERT (theme; Sandstorm related stuff, Onix/Steelix, Dunsparce, some fossils, Skarmory, Trapinchies)
#3: LEGENDS (5 Gen One, 5 Gen Two, 9 Gen Three, and 11 Gen Four (Manaphy, Phione, Heatran boxed elsewhere))
#4: Seafloor (deep sea fishies, fossils, Dratini, Manaphy/Phione)
#5: Seashore (ocean surface stuff, beachy things, shellfish and crustaceans)
#6: River (more water stuff with some inland stuff like Farfetch'd)
#7: Forest (basic Grasses, some bugs, Sudowoodo)
#8: Jungle (different Grasses, some bugs)
#9: Farm (farm animals, crop related things, some dogs and cats)
#10: Iceberg (Ice types and some Thick Fat and Clear Body)
#11: City (Psychics, Ghosts, and some Poisons)
#12: Sky (birds and flying Pokemon
#13: Starters (most starters, some boxed elsewhere)
#14: Volcano (Fires and some Rocks)
#15: Cave (Rocks, Zubat, Wobbuffet, Ursaring, Salamence, Sableye, Steels)
#16: Trades
#17: D.U.D.'s (stands for: "Daycare (projects), Unorthodogs (HM Slave Smeargle), and Dittto")
#18: ??? (stuff uncertain of where to shaft get put here)

Evolved Pokes are moved towards the box tops.
 
Right now I'm organizing them like you would do for pokemon cards. Like my "orange" box would be filled with ground,rock,and fighting types and my purple box would be filled with ghost, psychic and poison. I also have a box called "new" were all the new pokemon I catch go into temporarily, a "team" box were I have my teams stored, and a rare box filled with shiny and legendary pokemon.
 
I'll usually organize my PC boxes by Type, Events, and EV'd Pokémon. Then I'd make sure the background for each box match their titles accordingly. Right now, however, the only game I have that's actually organized is Diamond. My Platinum, SoulSilver, and White aren't as neatly placed yet; mostly because I'm currently replaying SoulSilver and I plan to restart Platinum and White again afterward and also because I never got around to doing it. /lazy
 
My boxes in my HeartGold version is a total mess lol, boxes are really not organized and I got like 12 boxes that are full, so It's a real hassle to find the Pokemon I'm looking for.

In Diamond tho, I got my boxes organized by Pokemon. Since I use that game for my trading thread, I put each starter in a specific box.

Same goes for my White version, but I have an extra box for my Dream World Pokemon.
 
This thread was active in the best year ever, but died then. So let's not post in it. Plus, I think there's a 2013 version of this floating around. :)

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