muscles that are in your upper back...
your rotator cuff muscles...
What hurts or is tight? Keep in mind that there is a difference between those two. When you go to touch your muscle and it hurts right away, then thats pain. If you go to touch your muscle you feel that is bugging you and there is no pain, then it is probably just tight and needs a good massage. However though, tightness for too long can cause problems. Always stretch after you workout and always warm up good dynamically before you work out. In my case, I have always had tightness and never pain even if I play softball all the time. I always massage my muscles and spend a little more time on a muscle I feel is tight.
In your case about the clicking in your shoulder. It can be a cartilage problem. Also, read this article called "The Clicking Shoulder".
The Clicking Shoulder | chiroweb.com I have clicking knees (no pain) and I am still trying to get rid of it because it is annoying.
Shoulder Symptons -
Shoulder Symptoms -- Pain, Weakness, and More -- JointHealing.com