Many of use MCs handheld "sync" to a viritual handheld (a directory) in order to manage the conversion from a lossless format (flac, etc.) to a compressed lossy format that the iPod can accept (mp3, etc.). So don't be dissuaded by the sync term.
After you have your collection of files that are candidates for the iPod, you can use iTunes to transfer the files that you've imported into iTunes.