The key to maintaining a stable and well functioning shoulder joint is keeping a strong supraspinatus. Unlike the other three muscles of the RC, the primary action of the supraspinatus is shoulder abduction in the scapular plane during the first 30 or so degrees of range of motion. It acts to normalize joint mechanics by keeping the head of the humerus seated within the glenoid fossa of the scapula and preventing the humeral head from gliding too far in the upward and anterior direction.
A weak supraspinatus is usually the culprit when there is an impingement problem in the shoulder that isn't the result of a traumatic injury or large bone spur. Typical rotation exercises, even when performed properly, do little to strengthen the supraspinatus. Neither do regular lateral raises.
What does work very well are a couple of exercises known as the empty can and full can, aka scaption exercises. They involve abduction of the shoulder in the scapular plane (about halfway between where you would lift for a lateral raise and a front raise). The empty can is performed with the shoulder in an internally rotated position with the thumb pointed down. The full can is performed with the shoulder in external rotation with the thumb pointed up.
With these exercises, maximum weight used will be 5 pounds--usually less--since heavier weights will end up recruiting the deltoids for the work. The lift goes no higher than 90 degrees, and less if there's pain--stay in the pain free range at all times. The goal with these exercises is improvement in local muscular endurance more than maximizing strength, so the reps are high--shooting for 2-3 sets of 15 to 10 to start, working up to 2-3 sets of 30. Early on, the exercises can be performed daily, since the muscle will typically be very easily fatigued and won't be able to tolerate much in terms of resistanc level or repetitions.
The exercises may be performed in standing, seated or prone (more advanced) using bands or weights. Keep them slow and controlled, especially on the eccentric part. Watch yourself in a mirror and make sure that you aren't getting the movement started by lifting your shoulders towards your ears--the motion has to be initiated by squeezing the shoulder blades back and down while lifting the arm.
Let me know if this isn't clear. Sometimes written descriptions without demos or pictures are a little difficult to understand.
Maribeth