The aluminum (or whatever material) jig doesn't have to be square - simply consistent - though being square certainly helps align to the corners of your workpiece. Mark the jig as to what the top outside corner should always "key" to -- in other words, if you use a square jig, and don't mark it for consistency in alignment, there will always be some margin of "play" in the way the workpiece is marked/drilled since you may inadvertently rotate the jig during workpiece marking. I used a 3" x 3" piece of aluminum with a thickness of around .0625" (1/16") , and cut a hole to size that matched (and some) the diameter at the tip of the forstner pilot arbor. This ensures that ALL the holes will line up consistently, since the pilot on a forstner extends perhaps a quarter inch below the actual cutting head. Be sure to mark (with tape et al) which side of your workpiece is your top, and then mark the edges (front or back). I tend to pick the best finish on any given workpiece, and then go from there. Since no piece of material is ever truly square in all dimensions, it helps to start at one corner, and "jig" around the workpiece clockwise so that each shelf is consistently marked and drilled. As long as everything is marked and well-planned, you'll have no problems.
-Richard
-Richard