Spin two nuts onto the bolt, tightening them against each other. Then chuck the bolt into the drill and hold a hacksaw blade against the spinning bolt. The nuts help to steady the blade and clean off burrs when you unscrew them.
Grab a compact disc (scratched ones that won’t play work just fine for this) and center it on the hole mark. As you drill the hole, watch the reflection in the CD—keep the bit in a straight line with its reflection for a perpendicular hole every time.