If you get your box squat to mimic your back squat you'll relieve your knees. In a box squat you're using hamstring and hips to leg curl up off the box. Take a vid from the side when you back squat. Watch how far your knees travel over the toes. If you can sit back more you'll get more power thru the heels and up the posterior chain. The quad strain is whats pulling on your knees.
HisAngriness complained of a similar problem of knee pain and I helped him box squat. It worked for him.
