Only 2 games I have my boxes organized.
Most other games I only catch Pokemon in random.
In my main Alpha Sapphire game, I do have boxes organized.
Boxes 1, 2, 3, and 4 - are my double battling various teams, so anyone who wishes to challenge me to more than 1 double battle, I can have lots of teams to choose from, for now have a total of 10 different teams.
for now Box 4 - are my other battling Pokemon I haven't yet added to a team
rest of the boxes, I may push a box down if I get more battling teams for now:
Box 5 - are my 5 Pokemon I have for contest, maxed out for their contest
Box 6 - teams I set aside for Theme Teams
Box 7 - various legendaries I caught in my other games
Boxes 8 to 22 - are empty for now
Box 23 - Bred Eevees
Box 24 - are Eeveelutions I have asked for from the GTS, or brought over from other games
Box 25 - are my Fennekin, Braixen, and Delphox from the GTS or other games
Box 26 - Zorua, Zoroark, Vulpix, and Delphox from either GTS, Zoroark event, and other games
Box 27 - Feline Pokemon I brought over from other games or got through Wonder Trade
Box 28 - Canines/Dogs I brought over or got in Wonder Trade
Box 29 and 30 - other Pokemon I like
Box 31 - are the Pokemon I brought from B/W/B2/W2 PokeTransporter
Battle Box - my AS double battle team, in case anyone challenges me to a battle while being online I don't have to waste time going to my PC battle.
Other team I have boxes organized is Pokemon X, the game I'm using for breeding.
I believe the first 20 or so boxes I have them organized by Pokemon that can have Male and Female - one of each evolution. After that I have a box of Pokemon that are Male only along with a Ditto - the next box Female only Pokemon and a Ditto - the next box are genderless Pokemon that can still breed.