Hi Martin and
to the forum.
As a 6S LiPo pack doesn't have a high enough voltage to work on the 24V setting, there's a possibility that a 12S LiPo pack won't work with the 48V setting either.
I would suggest programming the battery voltage setting on the controller to 36V and then use a separate
battery monitoring device that simply plugs into the balance lead on one of the 6S packs
(or use two units to monitor both packs if necessary).
Using two 6S packs connected in series to produce a 12S pack would be easier to charge, as it can easily be reconfigured as a 6S2P pack for simultaneous charging.
Trying to charge a 6S and 7S
(4S+3S) pack could be a real pain.
I am currently in the process of building a 5Ah 8S pack from a couple of 4S hard packs for use with my MPIII, but I have been using 7S and 14S packs on my earlier Pies without any problem for the last couple of years.
Alan