1) Practice. Do your squats suck because you're weak? Because they feel awkward? Because they make you sore? Practice will make all of that better. Squat. Squat in the gym. Instead of bending over to pick up something little, squat. Take a broom or mop handle or PVC pipe and practice your form while you watch TV. Strength is a skill. Powerlifts require (at least some) technique. Practice with good form provides both.
2) Do no do static stretches before you lift. You should be doing light weight warm-up sets before your actual working sets (warm-up sets don't count) and doing dynamic movements to limber up is fine too, but save any static stretching for after you lift.
3) If your ankle flexibility is shyt, consider squatting with two small plates under your heels. Work on increasing your ankle flexibility during random "down time" (sitting at a desk, watching TV, w/e) by doing specific ankle mobilization exercises.
4) Never squat in running shoes. Use a shoe with a flat, noncompressible sole.
5) Don't cheat reps. If the crease of your hips was above the top of your knee, you're doing it wrong. Your ass doesn't have to be touching your calves but half-squatting will only place additional strain on certain parts of your knee and will not make you a better squatter. Don't do it.
What else would you like to know?
