I generally organise my boxes, as 1-30, for Box One, 31-60 for Box Two, and repeat all the way up to 493, in the spare space on the 481-493 Boxes I put extras, I have, such as the Level 1 Regigigas (From SnowPoint Temple) I have, and the Level 100 (Not legit) 11th Movie Regigigas (Thanks to UnderXRay there ) then in my final box, I call it "New" and exit, and just let the new guys I catch go in there for sorting.
The only other time I've changed this is to show a friend all the legends I've got from UnderXRay, where I made a Legends box and moved them all into there.