I've had knee issues for years but I can still comfortably ride with MTB clipless pedals and cleats.. What I do is sit on a barstool or a countertop edge and let your feet hang freely. You'll be able to see each foots resting position. From there just adjust the cleat so it allows the proper angle for each foot.
Also check seat height and make sure it's not to high or to low.
If you use clipless make sure the cleats are properly aligned with the pedal shaft and the ball of your feet.
Here is a descent video to watch on cleat placement..