The only way to protect your knees is to use good form. Most people just "
sit down" when squatting instead of "sitting back". This is the easiest way
to get your knees over your toes and have knee pain from squatting.
The correct way to squat is always initiating the movement with your hips by
sitting back first. Then instead of sitting down, you would try REALLY HARD
to keep your knees out toward the side when you descend.
The following video explains it best:
