You don't lose any rune regen as long as one rune of a given type is recharging. As it also eliminates human error, B is the best option. I don't dispute that C is theoretically superior-- it is. It's just not worthwhile in practice.
Note this sidebar is completely separate from macroed vs. manual BT for the purpose of creating 6 Blood runes for sustained AE. That's still up in the air.