Yes, I would fuse both batteries with one fuse at the max draw you expect. In your case it may be only30 to 40 amps. There are DC circuit breakers which can be mounted on the surface with terminals in back or terminals on the face. You may design a panel on the box where you have the batteries. With the lower current you can also use the circuit breaker as a disconnect.
Look at the Blue Seas 285 or 187 series, and the C panel mounts, with toggle switch. I use both of these. The C series where there may be multiple circuits. The Blue Seas Web site is the best place to compare. Be careful of Chinese imitators.
This breaker should be as close to the battery as possible. You are fusing to protect the wire--if the wire draws over XX amount of current, you want that flow interrupted before the wire becomes a hot glowing heat element (and that can happen rapidly in a full short)
I have much higher current potential draw--the Victron Inverter also will boost current and voltage, so there can be sudden surge loads on it. Thus a larger fuse, rather than a breaker.
I understand your concern about the box. I prefer plastic junction boxes. There are many outdoor type of plastic boxes at Home Depot or Lowes, where you can make water tight connections, which will serve you much better in an out of body type of mount--be in under or over, or in a compartment where there is risk of water intrusion.
Another concern with a metal box and potential issues with wire insulation failure, is that the metal box may be grounded--and the positive wire short to that box. The grounding may be where the box bolts or screws onto the frame of the vehicle.
You are thinking and looking forward to make the installation as safe as possible. That is excellent.
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Bob Austin--celebrating 60 years of RVing
2013 Via 25T
Pensacola, FL
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