When shouldering any bike, I always have my hand up next to my shoulder so it actually takes a large part of the weight, and it is key to stopping the bike bumping up and down on my shoulder (which is what seems to cause the most discomfort)
Additionally, make sure the top tube rests on the top of your muscle, not actually on your shoulder itself. Muscles cope easily with a metal weight - bones not so much.
Finally, I always tilt mine down slightly to the front, this way I can get the tube to sit really nicely on my muscle without the pedal bashing me in the back.