how should the nock height be measured from a square? is it from where the bottom of the arrow sits on the shelf or from the center of the arrow?

I measure from the shelf to the bottom of the upper string nock, as do most archers. But, in reality, it doesn't matter as long as you always do it the same way. And, by all means, write it down so you don't have to trust your memory.

i do mine to the top of my nocking point...

That's interesting. I measure from the shelf to the bot. of the string nock also.
When I think about it; the result I am trying to accomplish is to get the nock end of the arrow higher than the point end, so it doesn't matter.
Agree with Joe. As long as you do it consistently...

The most useful square I have works with an actual arrow screwed onto it...in the end though I find as long as the nocking point is on the high side it is not too critical for my shooting purposes

DDave

this is the picture im confused on, its saying measure from the center of the arrow a half inch.
https://www.google.com/search?q=recurve+half+inch+from+center&espv=2&biw=1920&bih=979&tbm=isch&imgil=5A079RY0YVmplM%253A%253BO_pgm02NlMqDJM%253Bhttp%25253A%25252F%25252Fwww.bestrec urvebowguide.com%25252Ftuning-your-recurve-bow-part-1%25252F&source=iu&pf=m&fir=5A079RY0YVmplM%253A%252CO_pgm02NlMqDJM%252C_&usg=__3IdJ7vVJTOymCWWrLGZjFTgI-8c%3D&dpr=1&ved=0ahUKEwj kp6zNnoXNAhVFWD4KHSc2DZkQyjcIYg&ei=nv9NV-TgCcWw-QGn7LTICQ#imgrc=5A079RY0YVmplM%3A

Like Joe I measure to bottom of top knocking point and put on 2 nocking points (above/below) shooting three under.

In your link lay the square on the riser and measure were the bottom of nock point, same place as top of arrow nock would be, and mark it down along with brace. As stated goal is to know how to get nocking point in the same place repeatedly.