The way you set up is all about getting your body into the right position to give yourself the best chance at making a good shot, so you will want to make sure your shoulders are in the correct place to start off and that they are parallel with your line of aim.
Your shoulders should return to a similar position at setup as they do at impact with the ball, so you will want to keep them in line with your target to hit an accurate shot.
It's important to remember that the shoulders in the golf swing rotate on a tilted plane, established by the angle of your spine at setup.
A typical golf stance sees the upper body leaning forward, placing your shoulders roughly above your toes for most shots except the scenario where you find your ball sitting on an uneven lie on the course, then your shoulders should match the angle of the slope you stand on to play the shot so as to be able to swing with the slope, not against it.
Most golf shots require you to hit down on the ball, so having your shoulders level with each other at setup is appropriate for the majority of the time.
However, certain shots, such as a teed-up drive or fairway wood, might require you to lean away from their target slightly at address to help promote hitting up on the ball, therefore seeing the back shoulder slightly lower than the front at setup.
Out of Bounds: I had a caddie who once said to me walking up the second hole: "I used to be indecisive but now I'm not sure." Needles to say I shot an 81.