You will join the yarn for the centre stitches so that they can then be bound off but your yarn will be in the correct place to create the second shoulder. This is done in the same manner that you would join a ball of yarn for any part of a pattern when it is needed. Be sure to leave enough of the tail for weaving in later.
You have the option of either working both sides at the same time with both balls of yarn or you can work one side and then the other - the choice is yours.
The shaping that you do for one shoulder will be the opposite of what you will do for the second so that they match.