Hi KMunch,
I'm just learning about bare shaft tuning myself. I've been using OL Adcock's method. He advocates shooting 3-4 identical arrows (of each: both fletched and unfletched), then comparing the relationship of the groups. He also says not to pay much attention to the angle at which the bare shafts stick into the target.
If the fletched arrows are grouping below the bare shafts, then the nocking point needs to be raised. If the fletched arrows are grouping above the bare shafts, then the nocking point needs to be lowered.
The entire process is written at:
http://bowmaker.net/tuning.htm Hope this helps. There are others here who are vastly more experienced than am I, so hopefully, they'll chime in too!