Take your shoes and socks off, place a tall mirror on the floor so that you can see yourself fom the waist down, walk around a little bit to loosen up, and then casually and normally walk toward the mirror and have a look at the alignment of your leg and angle of your feet. Stop when you get closer to the mirror and look down at your feet and legs to see the alignment and angles.
If it helps, position a camera low to take photos of your legs and feet.
What you'll discover is your natural alignment. Now align your cleats to match that reasonably closely.
But a question ... specifically where does your knee hurt?