Big time bareshaft tuner here. To answer the OP's question.
First thing I apply tape where the fletchings go that weighs the same.
Your supposed to get center shot set prior to bareshaft tuning.
Then any time during bareshaft shooting that the shaft hits higher or lower than fletched arrows, you need to bring bareshaft down or up to meet fletched arrows. Doesnt matter if its off to the side initially.
Then after bringing the two down together, then proceed to get windage together. If, during the process, bareshaft hits higher or lower, bring it back to meet the fletched arrows.
Bareshaft shooting and tuning requires the best form you can do. So dont make adjustments if one shaft hits off. It could very well be you. Shoot a couple of shafts and look for the trend.
Those are the basics. It be best if you do a little reading so you get a fuller understanding of bareshaft tuning. Its well worth doing IMO. But you need to know what to look for as far as arrow spine so your not chasing incorrect spine.