Download the appropriate EXE for your PPC off the PocketQuake website, then transfer the PAK0.pak and PAK1.pak files from the full version on your desktop PC to the appropriate directory on your PocketPC: \quake\ID1. You will probably want the files on a storage card in which case the directory should be \Storage Card\quake\ID1. You may also want to GZIP the files to make them smaller. You can get that from
http://www.gzip.org