You should pedal with the ball of your foot, not your arch. The ankle is the fulcrum for the force you generate with your feet. The ball of your foot is further away from the ankle than your arch so you generate far more force with the ball of your foot.
As you straighten your knee, pedal at a 45 degree angle down and forward for the greatest force. Bicycle shoes have cleats that attach to the pedals to keep the ball of your foot over the pedal, where you generate the most force. Don't wear soft-soled shoes that allow the pedals to press against your feet, which can cause pain. Experienced riders know that you should not bend your foot up when you pedal up because it wastes energy and tires you earlier.