Vocal sync aligns the audio from one track termed the "dub track", using the timing info (onsets) present in another track termed the "guide track". There are always two separate tracks you are dealing with. The "hybrid UI" dual waveforms are shown on the vocalsync region only for the purpose of allowing you to
visually align the data.
The audio is still the dub track audio but aligned in time using the onsets from the guide track.
How you use it is completely up to the application. You might want to align one track to another and then discard the guide track, or you might want to use it for double tracking. There are no rules to how you use it.