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When you sync with your iTunes library, SuperSync automatically adds new tracks to iTunes when it is done receiving a new track by upload and when it has finished downloading a new track from a remote library.
After each synchronization, you can check to see if iTunes is still updating. This is shown in the Transfer Status window, under iTunes Updates. Or check the iTunes status, by selecting the Status -> iTunes menu (+7)
You can also just look at the number of tracks displayed at the bottom of your iTunes application window. The total song count should increase with each update.
Do not quit SuperSync while it is updating your iTunes library or you will need to rescan your library when you restart SuperSync. You may want to wait until iTunes is no longer updating before starting another update, however this is not required. When updating a large local library, adding each individual track to iTunes will take progressively longer.