I’ve had some knee problems recently, and have worked through them with the help of my Chiropractor.
My right knee has always had a tendency for patellar tendonitis, and my chiro gave me a 3mm lift for me shoes, and that has helped a great deal. Turns out my hip is off by 7 & 5mm at my lower and top of my hip, making my leg shorter. He suspects I also may have had Osgood Schlatter disease when I was younger, contributing to my right knee giving me some chronic problems. One thing that has helped me also is skin rolling. My Chiro showed me how to do it: you take your fingers and tightly roll your skin and travel down the muscle. For instance, for my right knee, he found that the lower part of my quad was adhered to the fascia tissue. This happens when old injuries don’t heal properly. If you’ve got any tissue that has healed and “glued” itself to the fascia, proper skin rolling will HURT LIKE HELL in these areas. If you find areas that are like this, work them for a while and leave them alone for a couple of days, then try again. Eventually you’ll work the tissue free, it will heal and you’ll be less injury prone in that area. After a couple of weeks (maybe less) you should be able to roll those areas without any pain.
You can also buy a foam roller pad that will release fascia tissue. Do a Froogle search for “Myofascial Release foam roller” and you’ll find items that will be useful.
Bottom line, find out if you have anything going on structurally that needs realignment, lay off squats until your knees feel better, and try the skin rolling or myofascial release.
Hope this helps.