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Organizing your PC

My shinies are a in a dedicated box (the last one) and the gift, stationary starting from first one ordered by Pokédex number.
 
Honestly it made most sense to me to organize them by level, unless there was something else relevant. I did 1-9, 10-19, all the way up until 90-100. Then I realised how few Pokémon over 60 I'd get, so I saved space by making a 70-100 box. Honestly I only use that if I'm boxing a party member for some reason. Other than that, I just have separate boxes for any Pokémon I'm using in breeding/I've bred.

Edit: I thought you might be wondering - I do have more Pokémon than will fit in one box for one of those level groups, so then I split things up more than by groups of 10 - often random-seeming level spectrums depending on what makes Pokémon most evenly distributed. Either that or just have multiple boxes for the same level group.
 
Box 1 is always the 'Friends' box where I place all pokemon I have used in some shape or form during the journey. Box 2 will become part 2 of this if I fill up the first box. After that I will split up boxes into types. Types that don't have a lot of pokemon will usually get put together in a box to save space. If I'm playing a nuzlocke, the last box or two will be my graveyard for the fallen pokemon.

I also usually end up with 1 or 2 boxes of 'trade fodder' for wonder trade stuff.
 
I am rather OCD so I tend to organize by Dex number. If there’s multiple Dexes or a regional Dex and then the national Dex, I’ll go in order and then do National Dex last. I save my shinies for the last few boxes. And I put my competitive or random wonder trade Pokémon in some random box in between.
 
In gen 4 I organized by level, and then realized that was stupid.

For gens 5-7 my first box was "party rotation," any boxes to the right were anything wild caught in the game, immediate to the left of party was legendaries, and then to the left of those were the dozen or so boxes of all my old stuff.

In Sword I decided to finally do it and the "wild" boxes have been organized by type.
 
In gen 4 I organized by level, and then realized that was stupid.

For gens 5-7 my first box was "party rotation," any boxes to the right were anything wild caught in the game, immediate to the left of party was legendaries, and then to the left of those were the dozen or so boxes of all my old stuff.

In Sword I decided to finally do it and the "wild" boxes have been organized by type.
I tried organizing by type in one game, but I found it much harder to find anything. I think mostly because there's no particular order for types to be in. Like, I'm at Steel or Fairy for example, and I have no idea what direction Grass or Fire is. I generally know the approximate level of a Pokémon I'm looking for, and as levels are ordered low to high I know exactly which direction to go in. It's just much easier.
 
I tried organizing by type in one game, but I found it much harder to find anything. I think mostly because there's no particular order for types to be in. Like, I'm at Steel or Fairy for example, and I have no idea what direction Grass or Fire is. I generally know the approximate level of a Pokémon I'm looking for, and as levels are ordered low to high I know exactly which direction to go in. It's just much easier.
You know, that's perfectly fair! I didn't mean to imply that organizing by level was stupid for everybody! I just tried to level up most of my stuff to about the same level so a bunch of my boxes were really thin and some I had to double cuz I had so many. For me, the type order, I definitely understand at first, but for me I picked a sort of natural "in-game" order, based on things like the themed backgrounds and the outfits for gyms and stuff, and really the only way to make sense of that order was too get used to it, which I have at this point. Of course, you could always go alphabetical. Then you always know where the others would be in relation to each other.
 
I have three main boxes: a to-do one, where I keep Pokémon I want to evolve, train, whatever. I have a favorites box, where I keep the original playthrough team of the game and others I just really like, and a box for legendaries. Other than that, it’s just a mess.
 
Box 1 is my de facto "in progress" box, as in these are Pokemon I'm currently working on, leveling, EVs, hyper training, TRs, ability capsules/patches etc.

Box 2-3 I just have named "Teams" these are all my in-game teams since Gen 6 in order, all of them are competitively viable. Box 4-5 is named "Legendaries". Legendaries from my journeys since Gen 6 as well, in Pokedex order. Box 6 is "Events" this is where legendaries or mythicals not in my OT go, things like event Celebi, Jirachi, Rayquaza with V-create, etc. Box 7-8 is "Duplicates", typically these are legendaries I've caught multiples of and I store the multiples in their own box rather than stuffing them with the Legendaries boxes. After those 8 boxes, everything else is just random stuff I've caught, I think Box 9 is a breeding box with some Pokemon I used to chain breed egg moves plus a perfect IV Ditto.
 
I tried organizing by type in one game, but I found it much harder to find anything. I think mostly because there's no particular order for types to be in. Like, I'm at Steel or Fairy for example, and I have no idea what direction Grass or Fire is. I generally know the approximate level of a Pokémon I'm looking for, and as levels are ordered low to high I know exactly which direction to go in. It's just much easier.
That's why I use the gym order: Rock, Water, Electric, Grass, Poison, Psychic, Fire, Ground, Flying, Bug, Normal, Ghost, Fighting, Steel, Ice, Dragon, Dark*, Fairy.

*I know Dark only got a Gym recently, but it was introduced before Fairy and I'm too used to that order to change it.
 
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