You should mount a rest so that with an arrow nocked onto the string at 90 degrees to the string the arrow approximately bisects the rest mounting hole(s).

Whereas the bottom of the arrow sits on the rest the nocking point is located on top of the nock on the string. This is why you hear suggestions that the nocking point should be 1/8" or so above square. What you are doing is making the arrow perpendicular to the string.

This is a starting point for nock location. As you tune your bow you may have to move the nocking point up or down a little for best arrow flight.

NOW----here's the part that should answer your question. Once the bow is tuned you do not move the nocking point. This has nothing to do with how your sight is located on the bow.

In your case, the sight is high in the sight window (if I read your post right). This is because your anchor is too low. You can raise your anchor which will point the bow downward more and the sight will have to be moved down to compensate for it. In raising the anchor you will also have to lower your peep and kisser button.

In some cases, depending on the A2A of the bow and such you even may have to shorten the draw length of the bow some to get the proper results. I almost think this is part of your problem. So you may have to do all I mentioned to get the desired results.

Believe me, it's not the fault of the equipment but one of form.