The first thing I would do is make sure you are doing the PISTON squat, and not the Pistol squat. Two very different movements!
The piston squat is great for building the quads, while the pistol squat is a single leg movement requiring a lot of mobility and places a large amount of sheer force on the knee.
Here is a link to each movement
If you are in fact doing a PISTON squat, and are having knee pain, I would make sure that you are sitting back into the squat as you normally would, in order to tension the hamstrings. If you continue to have some knee pain, I think taking some time away from the movement, performing some corrective exercise like TKE and glute med activation to relieve the strain on the patellar tendon. It may not be the most optimal movement for you.
Paul is an elite level raw Powerlifter with personal bests of an 805lbs squat, 440lbs bench, 725lbs deadlift and a 1960lbs total in the 242lbs class, as well as an 800lbs squat, 430lbs bench, 700lbs deadlift and 1930lbs total in the 220lbs class.
Paul brings a deep educational background to the team as he has earned Master’s degrees in both Sports Management and Exercise Science. He is a former D1 Collegiate Strength and Conditioning Coach, who now works as a Functional Rehabilitation Specialist in Calgary, Alberta, Canada.
Paul provides coaching services in the areas of training and nutrition through his company Master Athletic Performance and is also the co-founder of a technology company, 1-Life Inc. Stay tuned for more information on that in the future!