Starrman,
A good place to find the definitive "6 volt in series" info is the web site of your battery manufacturer or here as an example from the Trojan Battery site:
https://www.trojanbattery.com/pdf/Tr...UsersGuide.pdf
Note the torque values and wiring diagrams. All important stuff.
I have never taken load off my battery bank other than at the "terminal" terminals as indicated in the diagrams. You need both batteries in the "loop" to achieve 12 volts; someone more clever than me might have an idea for you.
Clearance to avoid metal to metal contact should be maintained by the hold down system in the box. If your measurement of box height and battery terminal height indicates they will contact, you will have to address that - some here have added aluminum channel around the top of the battery box, after drilling out the lid hinge attachment rivets, and re-riveted the lid hinges to the aluminum channel. Search battery box modification in the forum.
Even with ample clearance, I tend to cover the exposed terminals at the negative and positive connections to the coach with a rubber cover. Call me belt and suspenders guy. Also helps prevent inadvertent contact while I am working inside there.