This is something I ended up messing around with recently.
Basically on the Wrangler the auxiliary battery is connected in parallel to the main battery almost all of the time, with the two being separated briefly during the engine start (where the voltages can be checked separately) and during an Engine-Start-Stop event (where the aux battery is used to power the cabin load, eg items like the air blower fan, radio/onboard entertainment etc) such that the main battery is preserved for cranking the engine.
If the auxiliary battery or main battery goes bad (happens reasonably often), because they sit in parallel most of the time, they’ll tend to kill the other battery fairly quickly. That’s how you often end up having to change both at the same time.
As an FYI, if anyone should wish to change the aux battery themselves, it’s easier to remove the fender (four bolts, one push pin, and replace a few clips on the reinstall) and drop the battery tray…looks extreme but it’s a fairly easy job and can be done in under an hour:
The access from below is much easier than pulling out the fusebox.
You could also isolate the aux battery and disable it…
There’s an argument to be made that the incorporation of a second battery in this way (dissimilar sized batteries running in parallel) is a really bad piece of design that was rushed into place to meet restrictive US automotive emissions regulations.
There’s a negative cable that runs from the aux battery to the main. If you disconnect and isolate that, remove fuse F42, and persistently disable ESS (using eg a Tazer JL Mini), then your car will happily run on the main battery only - and probably have much longer battery life in that setup.
However there’s also a good argument to be made to just leave it as it is and lean on the warranty!