We are currently experiencing a flood of requests from bots scraping the forums. Unfortunately it has gotten to the point where it is negatively impacting the site. As a result the forums may be slow and you may periodically experiance an error message.
We are aware of the problem and apologize for the inconvenience.
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.