Actaully, a trick I learnerd from one of my instructors 6-7 years ago is that you should really be moving your feet around depending on what your doing on track...
Whenever possbile you should have the arch of your foot on the peg, not the ball. The only time you should have the ball of your foot on the peg is during corning, and then the inside foot only. Keeping the arch of your foot on the peg gives access to significanly more force that can be applied to the - i.e. with the ball of your foot, you're using your ankle, which really isn't "that" strong, but when you have the arch on the peg, you are using your thigh muscles, which are signifantly stronger than the ankle.
As far as the actual position, durning cornering - inside foot, usign the balls of your feet are perference for 2 reasons - the fore mentioned toe-clearence issue, and also as c-dub mentioned the ability to rotate to get you're toe pointed outward (in releation to the bike).