Your nocking point should be set so your arrow is a bit above horizontal or square on the string so your arrow will lift off the shelf. This will vary some with the tune of individual arrows and your personal release form.

How nock height measurements are taken vary from archer to archer. Also it will change depending upon your arrows diameter. I like to take mine from the top of the shelf, mark that height on my bow square so I can check it easily. Some guys take theirs from the top of the arrow or arrow centerline. I figure the shelf is always in the same place so I use that for my reference once I find the right height for a particular arrow.