It used to be that the soundtrack was copied to the duplicate negative, but only for B&W and certainly not in the last fifty years or so. I see this configuration only on very old archive material in B&W from the 1950s or before. Currently all soundtracks are printed from a separate sound negative that can be used with the original negative (if suitable for printing) or from the duplicate negative. Friends in large labs told me they could strike about 2500 prints from one set of duplicate negatives.
A separate sound printer head is used because the exposure of the soundtrack is quite different from the picture. Also, light changes in the picture would do no good in the soundtrack.