Start your squat from scratch. I had patella tendonopathy for 2 years in my right knee. Initially I worked single leg standing squat forcusing on the eccentric motion single leg and then standing up with both legs. I would stand on a small step and with a single leg squat down until my non active leg touched the floor working up to sets of 15. I performed these with my non-active leg going in front of me, to the side of the step and behind me.
I also performed squats on a 45 degree incline (initailly I rolled up a thick magazine or towel to lift my heels). Again the focus was on the eccentric loading of the patella, SO glutes contracted abs tight striaght back its all about the knee, not allowing my ass to stick out and back really hit the tendon hard. The advice I was given by my physio was if the soreness lasted more that 24 hours I had to rest a day, if 24 hours I was fine... hit them again. Therefore I trained them every day. Ice and NSAIDS were useful initially when starting out.
http://youtu.be/GiMnCi-fCvM (example video)
http://youtu.be/wY98htXP0O4 (adding weight in a rucksack to increase the stress on the tendon
I progressed this on to front squats with my heels raised and currently perform 3 x 60kg focusing on form and I still really feel this in the tendon.
http://youtu.be/4_UY8xtPpY0 (this is a little high in terms of step height but his back is vertical and all the movement is focused on hips and knee which is perfect)
My back squat is now back up to 140kg 5 x 5, I also lunge with dumbells, 3 sets of 15 each leg and finish each set with 10 jump squats to add a plyo emlement into the work (but I didnt do the plyo until a good 12 months into the training) 10kg dumbells.
I stopped any running and used rowing as my cardio (no impact on the tendon!) I also used to foam roll all IT band, hamstrings, quads adductors every other day.
Slowly but surely I recovered.
Taping and support I bought load of K Tape, my physio showed me how to tape up, it was tricky to start with if you are hairy youll be best to shave or at least trim your legs to get a better sticky. The taping lasted 48-72 hours, it lifted my petella but I wouldnt say it worked any magic.
http://youtu.be/xzDvY6Vr_uI (taping example)
http://youtu.be/aPkmo5Xqqtw (taping example)
I also bought insoles which supported my flat arches, these helped. but finding shoes that then fit is a pain in the ...er knee!!
Hope this helps. The biggest thing is to be patient with it and start from scratch to fully rehab it.