It has always been tricky to find a way to sync ipods in Linux, but I’ve found a way.
1. Get Amarok (version >= 1.4.4)
2. Make sure you have libipod installed – this allows iPod file functions.
3. Initialise all music in Amarok.
4. Initialise iPod
5. Goto ‘Playlist’ on the left menu bar
6. Under ‘Smart Play lists’ -> Collection -> All Collection.
7. Right click -> Synchronise to media device.
8. Goto ‘Media device’ on left menu bar.
9. At the bottom of the left pane under ‘Transfer Queue’ it should now read ‘All Collection’
10. Underneath the top menu bar select ‘Transfer’
Sorted!