I'm back. About PokéMon, their individual folders go into pf/item, and each folder has to be named properly. The file you put in these folders must be named as "Pkm*POKÉMON NAME*Brres.pac.
For example, a Torchic hack should be named PkmAchamoBrres.pac, and goes in pf/item/achamo, since Achamo is Torchic's Japanese name. In the Shiny PokéMon Pack, you have to rename every file that says, for example, "Shinytorchic," so that it matches its actual name on the ISO, in this case, "PkmAchamoBrres.pac.
Assist Trophy Characters also follow a similar rule, but their file must be called Asf*ASSIST NAME*Brres.pac
To make your life easier (and mine a bit more difficult for the next 3 and a half hours that I'm typing this), here are the proper names for each PokéMon AND Assist Trophy.