My first concern with a 2-battery setup was how to safely enforce that only one battery be enabled at a time and absolutely no possibility of shorting power to ground. I didn't like any of the high-watt switches or relays out there. Well, there really aren't any 50A DC switches and the relays I found where expensive ($50) and resistive...tended to heat up. We found these ports and will create a jumper (below) to use as an ARM-ing switch. We didn't want to use XT60 ports as the arming jumper because we're using XT60 ports for the battery charger. Accidentally jumper-ing (shorting) the charge port would likely create a LIPO fire. This way, there is no way to mistakenly do arm the wrong port.
We only made one jumper so you can't enable both batteries at the same time. To run battery 1 or 2 put the jumper in jumper slot 1 or 2. To charge just remove the jumper and plug in the charger to either port.
Here is wiring schematic Next time, I'll just hand-draw it.