Depends on what kind of shafts and nocks you're using. With doweled commercial shafts or hand-planed shafts from boards, if you're cutting self nocks, you want to cut the groove across the grain so that the shaft doesn't split on you. With cane or shoot shafts it doesn't make much difference which way you align the nock, except that many people like to put the stiffest side of the arrow against the bow. With broadheads or stone points, I usually align them with the string. Some people align them perpendicular to the string. It doesn't really matter as long as the point spins true with no wobble when you spin it on its tip.
