That's actually incorrect or at least partially.
A raised heel combined with a high on the back bar placement is the easiest way to squat very upright.
Classic examples are olympic weightlifters. Their shoes sport an easy 3/4" to 1" heel on them.
I squat pretty close to olympic style in converse chuck taylor's(classic cheap basketball shoes favored by many powerlifters), but they aren't ideal for closer stances or more upright squat styles. I currently have some nice olympic shoes on their way to me.
Trying to do a very upright squat in flat soled shoes causes a huge stretch in the calves and many people do not have the flexibility to pull this off right. I can from practice, but because of the angle of the shin and ankle in relation to your thigh and back it's extremely difficult to ever get really upright with any kind of weight on your back with flat soled shoes that makes you work hard. The flat soles and huge stretch on the calves causes most people including me to lean forward more than they would like even when you don't want to because your body forces you to.
Grab a broom and find a mirror or window you can see yourself sideways in. Place the broom on your upper back just under the bump at the bottom of your neck/upper back. That is part of your spine and you don't want weight sitting above or on that, but just under it. Your grip width should be comfortable, but tight enough that you can push your elbows back and feel a tight contraction in your traps and middle of the back.
Now stand sideways to a mirror/window. Looking at the mirror with the corner of your eye in the starting squat position, begin the descent by pushing your ass back first. As you push it back you will naturally lean forward the farther you push. While pushing back with your ass also start squatting down. What you should notice is that the ass goes back first, then the shoulder and head move forward and as this is happening you are descending down. Go as low as you can while keeping your back flat or slightly arched. Foot position will effect this. For upright squats heels shoulder width to a couple inches wider than that on each side seems to work best. You may be able to get your hamstrings to touch your calves.
If that is the case then you have good flexibility in the groin and lower body. But, while in the deep full squat position and with flat back evaluate your form? Are your shoulders past your knee caps? Does it appear your hips have rotated down and forward to achieve this depth?
Now place a solid flat object under each heel that is between 3/4" to 1" thick.
Squat again and notice how your body changes position as you descend into the squat with your heels now elevated. Now that you are in the full squat position your hamstringes should be easily touching your calves, you should have some forward lean, but less than when flat footed and your hips should be higher and back more than with flat feet.
Squatting with slightly elevated heels is not bad for you done properly. When you are in the full squat postion you should not feel any stress on the knees. The keys to this are to have your feet turned outwards between 15-30 degrees, heels shoulder width or slight wider and when you reach full depth your upper body should feel like its comfortably between your legs, not forcing itself down and on top of them.
Not squatting down and between your legs is how people hurt their knees. A classic example of how not to squat is toes straight forward, heel slightly inside of shoulder width and have some weight on the bar. Squat straight down. The knees end up moving forward first rather than the ass moving back. When you get into the full squat position your hamstrings are too tight against your calves which is exacerbated by the extra weight on your back which forces open the knee joint which in turn is not good.
Then to make matters worse people bounce down into the full squat position and bounce out of it all while using this stance style.
That is how knees get injured by squats. IMPROPERLY performed squats. Not necessarily elevated heels.
Now if you want to squat like a powerlifter then flat soled shoes are what you want because that is a wider stance squat that only needs the hip to get down to parallel or juuust under parallel where as a real full squat is quite abit deeper than that, but since It sounded like you want to squat more olympic or athletic style I tried to describe it as best I can.
Squatting is a very natural thing. Squatting with heavy weight on your back is not. If you were under a heavy beam and wanted to get it up higher you would get under it with relatively flat feet
and push your back flat against it and then push against it hard focusing on driving your legs into the ground rather than your back into the beam. Similar to the mechanic of a very heavy powerlifting squat. You can watch videos of all the greats and they all have quite alot of forward lean with heavy weight on their back. The key is the back may be leaned over alot, but it is flat still or slightly arched. This style cannot be done properly in raised heel shoes.
Hope this helps.
Please Scroll Down to See Forums Below 
