By the order in which they are caught. I tried actually arranging my boxes into types once, but it was just too much of a pain. Is it really that difficult to just scan each box for the Pokemon you want?
I arrange them in number order, with one box left for shinies at the end. I already know almost every Pokemon's number, so it's very conveinient for me.
I arrange it by type, and I have one egg box (if I get tired of hatching for a shiny, and have some eggs left, I put them there.) And once I get more shinies (if I ever WILL get more, I only have two ;_; ), I will make a shiny box.
By estimated habitat according to backgrounds. Then there's a box for the Pokemon I'm storing for my friend right now (He's got a shiny! So lucky..) and a box of legendaries and/or frontier usables/in training.
I arrange mine...well, to be blatantly honest, I don't arrange them at all. I will just let as many Pokemon occupy the box closest to the first one. The only organization I give my boxes is putting my main team Pokemon as separate from the rest of the Pokemon.
Though, if I were to arrange them I would probably do them by breeding groups, including a copy of dual-grouped Pokemon in each box.