A transfer punch fits snugly in an existing hole and precisely transfers the center of the hole to another surface when you strike it. You could just use a pencil to mark the hole; but then the holes don’t always align perfectly, which can be a huge PITA. When your holes absolutely, positively have to line up, grab a transfer punch set.
Because they’re designed to precisely fit in the hole, these punches are straight along the entire length, not tapered like most punches. This set from Grizzly includes 28 4-7/8″ long punches for hole sizes ranging from 3/32″ to 1/2″ by increments of 1/64.” The punches are slightly undersized so as not to bind in the holes.
You can get the Grizzly set or one like it for about $11 at many tool shops.