If somethings hurts, don't do it. Obviously you need to decide if its normal workout soreness or something more harmful. However, definitely check out the T-Nation youtube page. CT goes over in one of the videos exactly why he feels both methods you describe have negatives. CT recommends you use lifting straps to best protect your upper back as well as help the lift. This method still lays across the shoulders, however, so if you are experiencing pain from the bar there, maybe try padding. Personally, I had pain when I first started but am fine now.
Hopefully this helps you, since CT has been very busy and doesn't seem to check this forum. If you really want his advice, I suggest posting in his livespills.