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Yes, they are in parallel and need to be matched as closely as possible as the internal resistance will affect the charging rates just as one old but good battery can drag down a new battery.
Even if they're wired differently, the differing charging requirements of the two types of batteries means one of two things: Overall system voltage limited to lowest battery voltage, or LOTS of finicky electronics to limit voltage for one battery.
Freightliner tried it on my truck, and chose to limit overall system voltage. It winds up where your starting batteries are never fully charged, and so they deplete faster. The one battery that's supposed to support "hotel loads" when the truck is shut down lasts about 4 months, because you forget and try to start the truck on one horribly overloaded battery.
Freightliner gave up on the whole system in about 2 years, and reverted back to matched starting batteries. They also designed a small kit to re-wire the isolator system so that all 4 batteries would match.
The gel-cel they tried to use was like $250, and the 3 starting batteries were $120 each. You can rest assured that THAT bill was not fun at 0300......
To the OP: If you're trying to figure out a way to run your 12-volt accessories in a campsite or other venue, you have 2 choices: You can totally redesign your battery system to accommodate 6-volt lead-acid golf-cart batteries, which tolerate deep-discharge much better. Or you can set up a small isolated 12-volt circuit (much like the battery-charge wire in your 7-pin trailer harness) to charge a separate battery or bank of batteries while you're rolling.
The latter will cause you far less headache in the long run.
I'm not so sure that the charging of these two different types of batteries is a real issue (I maybe wrong) but my concern is a deep cycle battery isn't designed to provide a high inrush current to the starter while supporting the load of the glow plugs like a starting battery. Deep cycle batteries are best fitted for long duration loads at relative low current.
Best policy is the replace both batteries with the same type and technology.
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