Since I don't have many Pokemon in my Pearl version, I keep all of the ones I caught in the first box. I keep Pokemon that were traded to me from either the GTS or an in-game trainer in the second and third boxes. I traded a lot of junk over the GTS for more Trainer ID numbers and a better chance at the lotto, so.. Pokemon I breed are kept in my further boxes, such as boxes six through ten. I bred both types of Shellos, Gastly, Chatot and Gibles a year or two ago, and I still have their eggs in separate boxes; the "parents" I used for breeding are also together in their own box.
In my Platinum, the Pokemon I've caught are in the first box, as well as the ones I received from in-game trades. I caught all the Unown, unlike in Pearl, so I have them separated and organized in Box two. The third box is just for any extra Pokemon I catch or receive through any sort of trade.