If you have a consistent head position, it shouldn't matter whether your eye is over the arrow if you're focusing on the target and shooting instinctively. Shoot enough arrows and your brain should adjust. I think the best instinctive shots actually shoot this way.
However, I have found that I shoot much better, and have fewer misses to the left, if I position my eye over the arrow. When I do, the arrow seems to fly in a straight line from my bow to the target. I can tell if my eye is not centered over the arrow because the arrow seems to be flying from right to left, and often misses to the left. In order to center my eye over the arrow, I tilt my head slightly over the arrow.
Since it requires an extra movement, I would rather just hold my head where it naturally ends up when I anchor the arrow, but I have never been able to shoot as accurately that way as when I tilt my head so my eye is over the arrow. But you might try it both ways and see what works out best for you.