I installed iTunes this morning to sort it out. I'm glad I did, had a 7 hour journey to Hawkhurst for a wedding. Couldn't quite figure out iTunes so used Yamipod to copy the music across. Actually I used that for the first, Frozen, then it crashed, and I dragged the other folders straight to the IPod in iTunes.
Not sure if this is still the case now but when you plug in the ipod it will sync the iTunes library, that means that if the library is empty it wipes the ipod.