I generally believe that it is better to do your rotator cuff work prior to your workout as part of your warm up. You are generally working those muscles well below the fatigue threshold, so it shouldn't be an issue later in your workout. I also believe that you are neurologically improving firing patterns and that could help your workout.
Generally you want to avoid doing anything that irritates the shoulder ... so if you have pain during or after doing a particular movement, then avoid that movement for 2 weeks or so ...
I highly recommend this article that Bill Hartman and Mike Robertson wrote ...
Push Ups, Face Pulls, and Shrugs ... it might address a lot of your questions ...
One concern I have is what is causing your shoulder pain? Often rotator cuff problems are just a symptom of something else ... usually scapular instability or dyskinesia ... so doing rotator cuff work won't ultimately help unless you correct the scapular problems.