The Sensor is just that. It is attached to the Battery to monitor the Temperature so it doesn't matter where You connect it as long as it can "Feel" the Temperature.
Because Your Batteries are in separate Boxes You will need to decide which one to use. Or You could mount it between the two boxes if that is convenient. The fact that the Sensor has a Battery Terminal is because the Battery Post is an obvious point for attachment . it doesn't matter which Post that You use + or - is irrelevant !
Rob & Jean
98 Dutch Star Diesel Pusher ..07 Honda CRV AWD