If you have that kind of load that you will use for an extended time, you will want to make sure you connect through a 1-2 switch that allows you to switch between battery "banks".
When you have finished using the Aux batteries and if they don't have enough to start the truck, you can switch to second bank, fire up motor and then switch back to drained batteries to charge them. I imagine you could design or purchase a switching circuit for the "banks" that senses a predetermined "low voltage" limit and either cuts the power, or switches to other bank of batteries.
We have a 1-2 switch on a boat that uses a dual bank charger when the engine is running (12 volts). I can choose to run a single battery (in your case 2) or both bateries (in your case 4) with the switch.
A reference for you would be "skeeterboats, championboats, or basstracker" to see if they explain how the batteries are wired up to isolate when using trolling motors and not using big motor to charge.