If the inverters and batteries are totally independent (not in parallel or multi phase) then the GX device can only interface fully with one system. You can connect a mk3 to USB converter to the second inverter and connect this to the USB port of the GX device for monitoring only in the device list, no control via DVCC. The second inverter runs standalone. You can have a shunt on the second battery bank and this will be monitored and displayed in the device list, no control though.
The better way is to have a GX device on each system.
See Section 4.1 of the manual, plus the DVCC section.