Hi BFL13,
If the 12's are center tapped, the extra resistance in the cables to the six volts may tend to prevent them from becoming fully charged. The same thing happens when drawing from them. So the 12 volts will charge first--and that will taper the charge rate to the sixes.
If on the outer ends (method #2) then the 12 volt batteries will be the ones not getting fully charged--and not providing as much current.
I would balance the wiring myself. But that will cost you for cables. And the 12's were free.