I see...well, I do use Pokesav, but only to extract .pkm files. To be honest, I have exactly no idea how to use it other than the extracting part, so I don't even bother altering it.
EDIT: For some of my poke's (e.g. Oblivia Deoxys), they may turn out as 'Hacked or Unknown Pokemon'. This is normal, because it wasn't recognized at that time (don't know if a new version of Legal.exe is up, since I haven't checked in a while).