My 30 GB iPod has well over 100 playlists on it. Has had for years. No issues.
If you hit the storage limit (attempted to sync the entire library and it was too big to fit) iTunes usually will ask you if you want to create a playlist of the maximum amount of music and sync to it. Then you get a single playlist with most of your collection and it never changes. If you deleted that playlist, then nothing will sync to your iPod.
You should look at your sync options and either go back to syncing your whole library, or sync to specific playlists and select your playlists you created or go to manual management and drag and drop your songs and playlists to the iPod.
The "gear" playlists are smart, the "note" ones are static or unchanging.
Amazon songs have no DRM from what I see on some Google searches so they should import into iTunes just fine. Limewire songs used to be "flagged" by iTunes and would not sync, I don't know if that still happens or not. Personally I avoid Limewire.
My guess is you are syncing to nothing, and you need to adjust your sync properties. Check out the iLounge article on
Synchronization.