I'm one of the odd ones that does it by National Dex order, my bf does the same but sometimes he modifies it. I've tried modifying it too like to put new and old evolutions together, like Pikachu and Raichu with Pichu or the other way around.
I sorted it once by type and evolutions going down the way., twas freaky to say the least, lol ^.^
But not I sort them all out by National Dex order, and use the box that the Legendaries are in at the end like Giratina etc for my team when I'm breeding and keep the last box, box 18 for things I wanna level up and that I'm trading.
I lurve teh breeding, especially egg move breeding ^^
Anyway, cheerio!