I organize my boxes in a very specific way:
I first do types, (Grass, Fire, Water, Normal, Flying, Dark/Psych, GroRoFiSte, Dragon, Poison, Bug, ect.) which sometime smeans I have to make more boxes in the Grass/Water type because there SO many darn pokemon with that type. This usually occupies 8 boxes or so.
Then there's one for Legendaries.
And I made one just for Evee and its evolutions, though I might move them if I run out of room.
Then I have a box for pokemon I'm waiting to breed ith ditto to get an egg evo or the lower evos.
Then one for pokemon I need to lvl to evolve.
And that usually leaves a few boxes empty for extra storage. I tried once to organize them by lvl when I first got my Platnium, but having to constantly switch them when they lvled drov eme crazy and it's easier to find pokemon based on type.