Three blades- I align with fletching as the arrow is laid flat on the counter.
Twp blades- I align horizontally (perpendicular to bow string) as arrow is laid flat on the counter.
Only reason I run two blades horizontally is that cutting surface slides over my hand.
Aligning blades with fletching does not matter so long as the correct arrow is used and you have helical to spin it. However, I like them set the same so that once in the quiver, neither the blades not the feathers will rub each other.