How is the motor/center diff positioning looking?
If it is like your 1/8 set up, then I would guess one battery tray parallel to the motor on the opposite side of the chassis. The other battery tray in the back where the gas tank used to sit (perpendicular to the motor).
I will be using 8S via two packs of 4S, so two battery trays would be great. It will also help with the weight distribution.
Thank you for the love for our MCDs.