They show up in iTunes separately. iTunes can sync each one separately. To make it easier on yourself, you can change the name of your iPods in iTunes or in the Finder. Basically, it's like working with multiple connected disks or flash drives. Same idea.
Just make sure you set each iPod to "manual update" in the iPod prefs if you want to maintain different playlists or amounts of music on each.
From my one PowerBook, I sync up my 'Pod, a Shuffle, and my brother's 'Pod.