Stay away from the Smith machine. The only exercise I would consider doing on a smith machine is one legged squats. And even with that I would be reluctant to go on a smith machine. If you cant break parallel on squats you are simply using too much weight. Reduce the weight. It is my opinion that you can develop massive legs without a lot of weight on the squat. Please dont be afraid to do this. Most people dont squat anyway, so they wont have any right to make fun of you for using light weight. I have much more respect for someone who is squating just the bar with perfect form than someone who jerks up 1000lbs on the leg press.
To help you break parallel, try to actively pull yourself down with your hip flexors on the descent. When your abs have touched the top of your legs, you have hit parallel. Push up with the balls of your feet, NOT YOUR TOES. Innitiate the squat from the knees, do not buck your hips as this could lead to injury. Bucking the hips is tempting for people to do because it allows you to push up more weight. Dont do it.