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I organize my boxes in order of the national Dex (Regions). The first three boxes would be named Kanto with the Savannah background, the next three named Johto with the City background and so on.
Each space is one evolution line, for instance I don't have Squirtle, Wartortle and Blastoise in the same box, just one space represents all three.
The leftover boxes are designated to hold EV trained battle ready Pokemon, Unown forms, Dittos with different natures, Shinies that I've happen to come across, Foreign Pokemon, Hidden Abilities, Extra boxes for trades and a 'Trophy Case' for Pokemon I'll never let go!
Used to organize them by their rarity, but that quickly became hard to manage, sort of. Now, I organize them by types. I also set wallpapers to them accordingly. :]
I leave the backgrounds since I can't be bothered. I leave most monsters in the order they were caught, and place my main ones in reverse starting from the last box, in no particular order. This ended up being somewhat incompatible with the way extra boxes are unlocked once all the existing ones contain at least one monster each.
I organise them by usefulnes and how much I like them. My favourites and primo battlers go into the first few boxes- trade and breeding fodder get schlepped into the later ones.
I don't breed, so I normally have three boxes. The first is called "Random" with the forest background and is for holding Pokemon I like but don't want in my party at the time. Second is "Rare" with the river background for shinies, rare Pokemon, and Wondertrades. Third is "Legend" with the sky background for legendaries. :3
Well since I got Bank, I was able to organize my PC instead of having 31 unorganized boxes. Now I have boxes for competitive Pokemon, shiny non-competitive, legendaries, and random like lv 100s and HM slaves.
I organize mine by type with legendaries in a separate box. I like using the hidden backgrounds on my Legendaries, blue ones on Water types and so on. Depending on the game, I might not organize until after I've beaten the Elite Four.
I try and organize it by the level I caught a pokemon in, so usually by level as well. I don't care about backgrounds since I don't really spend a whole lot of time in the PC. If I have a longstanding member of my team that I "retire" I put it in its own box.
I generally organize by type. I like that we can reorganize boxes now in x/y so if my "water" box gets filled, I can name another box "water 2" and put it next to the first water box.
I keep separate boxes for Legendaries, shinies, breeding leftovers (thankfully can throw those all in the bank now) and my main team.
Now that I'm done Pokemon X, I should probably create an organized system of hoarding the Pokes \: At the moment, they're unintentionally organized by level because I still have the older ones sitting in the first box at low levels and the higher ones in newer boxes XD
Before I didn't organize my boxes, I would just move my favorite Pokemon the last box (prior to XY) everyone else just random.
Today I'm slightly more organized. I keep the first 9 boxes organized (see my examples & images below) - have other boxes for Friend Safari Pokemon, and the rest for wild caught Pokemon & Wonder Trades, and my final box, one before battle box Pokemon I set aside for trading.
My organized Boxes -
The first 8 boxes is where I put Pokemon based on their real-life animals. One for Pokemon based on mustelids & meerkats, the next for Pokemon based on cats, one for Eeveelutions and Pokemon based on foxes, the next box based on other canines that are not foxes, and the last one for what I call "PokeFriends" other Pokemon I like that don't fit in with the other boxes.
the next 3 boxes I have them organized for starters.
1st box organized based on Grass-Fire-Water like it has been introduced in every generation
from left to right - generation 1 to generation 6
next 3 - I have them by 1st evolution - middle evolution - final evoluton
images of my examples - you can also see what I use for the box's wallpaper:
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Box 1 - Mustelid Pokemon
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Box 2 - Feline Pokemon
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Box 3 - Eeveelutions & Foxes
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Box 4 - Canine Pokemon
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Box 5 - PokeFriends -
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Box 6 - Starters
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Box 7 - Grass Starter Pokemon
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Box 8 - Fire Starter Pokemon
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Box 9 - Water Starter Pokemon
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by the way, it took me over 18 hours to get every starter to their final stage
(hope my examples help out with my explanation)
The one in my PokemonBank I may start organizing them based on the DexNumbeers
In previous games, I just let them stay where they landed, so to speak, effectively putting them in the order that they were caught.
With the wonder Trade in XY giving me a huge surplus of pokémon (I'm one of those guys that trades away all my breeding spares), I've taken to organizing them by national dex number. I now know the annoyance of getting a rattata via wonder trade, only to have to move it through 20 PC boxes one by one so as to mot disrupt the order. XD
Some of my random Pokémon I put in normal boxes, but for cool Pokémon I can use seriously or that i'm collecting and such, i'll put them in boxes with special wallpapers. In my White 2 version, for example, I have lots of good IV'd Pokémon in the box with the Reshiram wallpaper, and a box of (pseudo-)legendaries in one with the White Kyurem wallpaper.
And in X, I use the wallpaper with the starters, and the one with Xerneas and Yveltal, all of which look incredible, for some of my best ones.
I used to not organize them at all. Now I organize them by team, meaning I'll have a whole team for each line in a box. This is useful since I'm at the stage in Pokemon Pearl where I've beaten the game and completed the Pokedex. Now I just level up a team and beat the Elite Four with it, before starting over with a new one.
When I was real into Black and White, I think I did on that game for the first time in many years. Normally, though I don't bother with them, they just stay in the order the game puts them in, so that I know the older / lower level ones are at the start, and the newer / higher levels are farther back. -w- That's about all I need, because it's what I've always been used to.
