On the "iTuner MP3 Synchronize" dialog window, clear the "Auto-detect folder capabilities" checkbox. Type the path or browse to the path of the target folder, select the folder layout template, and click the Sync button. While
it's not an automated, persistent configuration, it does provide the functionality you need.
Hope this helps.
I'm afraid that's just not worth it.
I'd have to click on the audiobooks playlist, then navigate to the audiobooks folder, then sync
Then I'd have to click on the podcasts playlist, then navigate the podcasts folder, then sync
Then I'd have to click on the music playlist, then navigate to the music folder then sync
I might as well do things manage my music manually or use another method (maybe syncing my playlists to another media player then syncing) if I'm going through all that.