I don't think it is possible to squat ATG without your knees going over your toes. The old, "don't let your knees go over your toes" isn't exactly the case. If you started your descent and your knees are very forward and you haven't reached parallel, that isn't good because all the weight is on your quads and knees. However, as you get lower into your squat (getting below parallel) your hips bear more of the weight.
Like the other guy said, you have to make sure you keep driving the weight through the heels. If you lack flexibility in any area, such as your ankles, your weight will be shifted forwards..very unsafe while squatting! Get familiar with just the bar in front and back squats and take it slow to get accustomed to the range of motion. Good luck.