If I understand you correctly, you are using iTunes to transfer music to your iPod, yes?
If so, you have to use the Tag Cache to view your collection, because iTunes scrambles the folder and filenames.
Once Tag Cache is up and running, you can use the dynamic playlisting or the Playlist Catalog from the Tag Cache browser to make On The Fly (OTF) playlists.
EDIT: Some info in the manual
here and
here