Two common setups require special note: iTunes by default uses your Document's Music directory for the primary location of your music. Often you'll dedicate a special hard drive for music, or use a network share. In both cases, you need to tell iTunes where your primary music library is so SuperSync can help keep track of additions and deletions.
When using a shared network drive, many users can have a copy of iTunes that points to the shared music directory on the NAS. The problem is that each user can have their own playlists, and new music that is added to the NAS is not reflected in all the other user's iTunes. SuperSync can help!
Change your iTunes music library location to the NAS music directory. This will tell SuperSync where to find all the music you are interested in. Go to iTunes, Edit -> Preferences... Change the iTunes Music Folder Location to the music directory on the network disk.
Hopefully most of your music is already in this location. Launch SuperSync and make sure it loads a copy of your iTunes library.
Periodically, you'll need to do a File -> Local Rescan to find any new music that has been added to the NAS. Any new music that it finds in your NAS will be added to SuperSync, and queued to be added to iTunes. Any music that is supposed to be in the NAS that is not will be removed from SuperSync and iTunes. As always, the first time you do a local rescan, do it in trial mode and review the changes that will be made when you're not in trial mode.
When connecting to another SuperSync, if you're both using the NAS for the music directory, you'll typically want to avoid copying songs that are already saved on the NAS. SuperSync will ignore or skip the transfer. But copying new music to the NAS will make it available to others after they do a rescan.