If you hook up two batteries together and let them sit, they will kill each other.
When you start your rig, it's nice to have two fully charged batteries together, but not a dead one and a good one.
In camp, you want them separated so you don't kill your starter battery, unless push/bump starting is really easy.
When winching, you want both batteries hooked up and ideally the engine running...unless you are underwater.
there are various ways to isolate two batteries. You can use an isolator, which makes your alternator work harder. Or, you can use a big relay which doesn't place a drain on the alternator. If you are using a relay, there are many ways to wire it. You may wire is so the two batteries are on when the ignition is set to run and/or start. Or it wires so that you have to flip a switch to connect them. The switch can be wired to power all the time or power when the vehicle is set to run, accessory, etc.
If it were my vehicle, I would like to know exactly how it is wired.