By Numerical Order in the first 13th boxes.
At the bottom of the 13th box I put Pokémon that I might trade.
The 14th box I used to put the Unown, but now that I transfered them to My Pokémon Ranch now I use that box for my Pokémon that I EV trained and aren't Lv. 100. When they reach to that level I put them in his numerical place.
All my EV Pokémon have a Heart Mark and the Trading Pokémon has a Star Mark in order to don't lose track of them.
If I have more than one of any kind of Pokémon and I'm not going to trade them, EV train them or use them for Breeding (Males with Egg Moves and Females with Good Nature), I transfer them to My Pokémon Ranch.
SoulSilver FC: 0732 7295 6417