Pretty much Jacob,
The alt doesn't provide that much power so its not neccessary to use a ton of batteries, but if you use more you get alot more life out of them.
So 2-3 batteries you might be able to avoid dropping into or below the 20% discharge and have a very long battery life. I think thats the only reason to use multiples, especially if the alts on a switch.
Some users on here have deleted it and removed the alt and the belts, so I understand that they wanted extra power because. . .well if the battery dies the car is stuck.
Other than that I would have the switch connect the deep cell when the alt is off(one switch or two switches side-by-side) to make sure you don't leave the deep cell on. I'd route it so that the deep cell being on means the starter battery is disengaged and the alt doesn't need alot of places to dump charge at that point the resistance in the battery is enough to fight it as well as recharging the battery(its probably not at 100% charge). This also keeps you from draining your cranker which won't survive cycle loading at all(I predict about 20 times but you might get 50 cycles out of it).
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