I feel obligated to reply. Don't go deep. Don't go below 90%. Yes, going deep is going to give you a greater range of motion and give you the best results BUT if you are having knee problems FORGET IT! You are either: a) damaging the meniscus tissue which may tear and cannot be fixed with surgery, or b) your patella(kneecap) is under too much strain.
I suffered patella instability for years but mine was due to a weak VMO muscle(the teardrop shaped quadriceps muscle that holds the patella in place). I strengthened it enough to do deep squats without trouble but I am half expecting trouble each time I add more weight. At the first sign of trouble I will be switching to 90 degree squats.