I had a serious rotator cuff injury 10 years ago that still keeps me up at night.
You are going to need two forms of attack
#1 Stretch before problematic exercises and warm up properly. Shoulder day and chest day I stretch like crazy and take my sweet time working up to a good weight. I have watched this video dozens of times. You need to do these stretches before you squat. I like to do them before I bench they are awesome
this dude is smart:
http://www.youtube.com/watch?v=scBJWKbUGX0
#2 You need to develop a rotator cuff strengthening regiment. You need to do a diverse range but the two you will want to start with are
inward motion:
http://www.youtube.com/watch?v=AEw-0wYGMXA&NR=1
outward motion:
http://www.youtube.com/watch?v=UwUBQqX5PrQ