I haven't used an iPod for ages. But it is possible to manually transfer to the iPod.
See this video tutorial from about half way through Apple - Support - iPod Tutorials - Downloading Music and Video It's my guess you have main library option ticked instead of just the playlist you wish to sync with your iPod. ie: with iPod selected, choose which selected playlist to sync.

This video tutorial shows option between automatic & manual synching of your ipod: http://www.apple.com/support/ipod/tu.../ipodsync.html & also mentions how to selectively choose playlists for auto synching.