The theory behind barefoot running is that the foot is the part of your body best designed to absorb shock while running. By running barefoot, you're strengthening the crucial shock absorbers, and relieving stress on the ankles, knees and hips. The thick-soled running shoes so many people use have been surmised by many physiologists recently to actually encourage more injuries to these other joints. If you want to just try the barefooting, but you don't have 1-inch callouses covering your feet, or a beautiful strip of soft soil/grass nearby, you can also strap on some thin-soled sprinting shoes. They have very little padding, and will help you get the same foot-muscle conditioning. When
running,
not sprinting, the foot naturally strikes the ground heel/midfoot first. It's virtually impossible to run any other way (this is NOT the same as sprinting, where you use the balls of your feet and toes as the primary springs to accelerate quickly.) Don't go out and try something as unnatural as running without letting your heel or midfoot hit the ground first. This will lead you to suffer some injury. Even when coaches say, 'run on the balls of your feet,' they're simply emphasizing you don't dig your heels in, which can be hard on you. But overcompensating by trying to run on your toes can be hard, too. Ultimately, you want to learn to run
most naturally. You want to learn better running technique, I highly recommend the Feldenkrais Method. A couple of classes geared towards running, plus some minimal shorter runs, you'll be breezing around and feeling like a gazelle. It'll also do wonders for minimizing the stress on your joints. I ran all through high school, college, and more, and I took a class a few years ago. I realized how much effort I had been wasting in bad/inefficient form. It teaches you to run a lot more with your shoulders, hips and core muscles. Here's the class I took to give you an idea:
http://www.balancedrunner.com/ The POSE system also looks intriguing.