Hey /vp/, how do you keep your boxes organized?

Personally I like to keep at least one copy of each Pokemon when I'm filling my dex so I can always have them on hand if I need to breed one for a trade or something.
I organize them in the National Dex order, but I only keep the highest evolution of the Pokemon to save room.
Then of course I have separate boxes for when I'm IV breeding, shiney hatching and a box for my fighters.