If you are using a bow square, it is very clearly marked so you know when you are 5/8" above "square", which is the same thing as being that distance above "level" or "center" (where the height of the rest would "center" on the string). Just a matter of semantics. As long as we all know the terms we are saying the same thing. And 5/8" is generally where I put the bottom of my upper nock set too -- I don't use a second, lower nock set unless I am using serving or dental floss for the nock sets.
Even if you put your nock set at 5/8" above square, leave it loose enough that you can screw it up and down on the serving until you achieve the best arrow flight. Then get some different weight field points and try changing those to see whether you can get better flight as you weaken or stiffen the spine. I would try a heavier field point and see if making the arrow spine weaker helps. If you notice a difference, use various weights to dial in the spine. This assumes you want to keep using the same arrows.
Allan