It's better to just do the shoulder fix program for at least the first two phases without doing other weight-lifting.
It'll help you get clarity on your shoulder issues and that'll help you also adjust your weight lifting in the future so you can stay impingement free for the long run.
Phase 3 does introduce weight-lifting / resistance training so that'll be a good time to pay attention as you transition into lifting weights again.
Remember if you cannot maintain good range of motion and good form, you may not be READY to lift heavy!