That probably only means that the 'louder' one is more microphonic so responds more to the tapping. I'd still stick the 6.8 one in the bridge and the 6.18 in the neck. If they end up sounding unbalanced then you can always swap them round.

I'd do the same with the Flying V - measure the resistance and put the higher value in the bridge position.

They wouldn't use different sized wire for the neck and bridge pickups, so the resistance is a good indicator here.