Re: Battries
I don't know specifics about the Roadtrek Agile, but in general the following is true:
The battery located under the driver's footwell area in a Sprinter is the vehicle's starter battery. The battery in the engine compartment is most likely an auxiliary battery, either one that MB put there or one that your coach conversion company put there.
If in fact the battery under the hood is an auxiliary battery (also known as the "house" battery in an RV) then it is probably being used to power RV devices (lights, pumps, accessories, things like that). It is separate from the starter battery so that it can be drawn down to a lower state of charge without compromising the vehicle's ability to start when needed. The auxiliary battery probably charges from the vehicle electrical system when your RV is running through the action of a relay. When the RV engine is shut off, the relay opens so that you can't draw down the starter battery.
(I think there are some people including myself who need to get a life...)