OMG MY ODDISH IS IN THE LAVA BACKGROUND!

[Heather]

Mine are completely random.. Usually I will make a box of my favorite pokemon and I will give them a really cool background for their box. :)

 

[Glameow]

I used to group them by type, but then I just changed them all to the beach background ~_~;;

 

[MarioManH]

I organize them typically by Shiny, Events, IV Breeds, Competitive, Shiny Competitive, and just throw everything else in random boxes.

 

[Oshakpop]

Organized mine by National Dex Number, then a box for Shinies, ones that aren't mine that I want to trade away, ones I have leftover that can't fit in the Natioanl Dex because there is already one of the same species, one for forms, ones I need to evolve, ones I need to breed.

 

[XpokeX]

I organise mine by their primary types,except for my party box and a breed box(all my failed Masuda method breeds go)

 

[Fernbutter]

I am probably a severe OCD freak and I end up using every background then renaming them all again. Afterwards I would just put them in the environment that fits them most.
If there are any extra unused backgrounds, the one remaining box will be constantly changed.