After drilling the first hole, move the board, drop the indexing pin into the hole and drill the next hole. Repeat the process for an evenly spaced row of holes.
The indexing pin should be the same diameter as the holes you want to drill into the board. Other important dimensions in this project are the distance from the fence to the bit, to make sure the holes are drilled into the board in the right place, and the distance from the indexing pin to the drill bit. That dimension dictates how far apart the holes will be.
Original article and pictures take http://www.diynetwork.com/how-to/skills-and-know-how/carpentry-and-woodworking/how-to-make-a-multiple-hole-jig site