I think you need to check the box in itunes thats says "use Ipod as hard disk" or something like that then it will act as a normal storage device and you should be able to use any software you want to sync it, media monkey is great if you have no need of videos.
This only works on the normal ipods not on the the touch, iphone and stuff but i'm not sure about the nano, worth a look though.
When I was playing around with my friends ipod touch I was able to sync/put music on it using media monkey without what I just wrote above, btw.