To get the most out of squat, you need to use your back, your abs, and your neck as well as your legs. Place the bar high on your lats rather than on your neck, be sure to keep a straight lower back, use a leg stance 1.5 times your shoulder width, place the weight on your heels, and have your feet in a 30 degree angle to the side. Use a belt when squatting heavy (be safe, not sorry), and always go below parallel. If you can't go below parallel, you shouldn't even be carrying the weight on your back in the first place.
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“He who controls the spice controls the universe.”