Assuming the wheel is true and properly dished and it's seated properly in the dropouts, you center direct pull, or V-, brakes, by adjusting a little screw near the pivot bolt on each arm. It's a spring tension screw; if you turn the screw in (clockwise), it tightens the spring, which pulls the respective arm away from the wheel. Try tightening the screw of the arm that is too close. If you get the screw in a ways and the arm is still too close, try loosening the screw on the other arm.

Edit, if you still can't get the pads centered, you can try rearranging the washers on the pads. Some pads have different sized washers that go on either side of the brake arm.