You should see a sports med doc. It sounds as if you have some chonic bio-mechanical issues.
With most knee problems, strengthening the quads is a good start. So, while you are waiting for your PT/sports med appointment, I would focus on doing exercises that will strengthen the quads - leg extensions, leg press, body squats, squats with only the bar, etc.
With patellar tendonitis it is a good idea to warm up your quads before going out for a run. Take a warm shower or bath before heading out our use a moist heat heating pad. Gently stretch your quads before running. Stretch your quads after running, then follow up with ice.