I shoot three bare shafts and at least three fletched together and compare the impact positions between the two. I work to get them grouping together, but I've found the most forgiving setup has my bare shafts grouping slightly right (weak) and slightly low (nock high) at 25 yards or beyond (I'm right handed). The bare and fletched groups overlap, but if you were to draw circles around them both and compare the center of each, the center of the bare shaft group would be slightly low right from the center of the fletched. It takes a while, usually several sessions of tweaking.
If I try to watch the arrow in flight is sometimes messes up my follow through which in turn sometimes causes the shaft to plane a bit...in other words looking for the arrow can introduce and uncontrolled variable for me. Besides, if the arrow is planning significantly it won't group with the fletched shafts anyway.