Where your nock point goes depends on if you knock on the bottom or the top of your nocking point. (John Schulz recommends nocking on the top. He says it is faster.).
Anyway, you want your arrow to be an 1/8, 3/16, or whatever, up from the arrow shelf. Just take the 5/16" (or whatever diameter arrow you shoot) and add the amount of rise you use to it. That is where your nocking point goes. Mark the string at this point. You decide if you want your nocking point above or below this mark.
-Ken