The nocking point should remain in the same place, once you have set the bow up correctly. That said, if you change limb weight, arrow weight or draw length, the nocking point may need to be adjusted again. Use a bow square to record your current nock height, then make minor adjustments until your arrows fly and hit horizontally. Low shooting can be caused by lots of different things, arrow weight/spine, bad form, drawing short, big sight picture. Try and get somebody to video your draw and release, diagnostics are easier when you can slow down the action and watch. It's quite scary to find out how many bad habits you didn't know you had!