You can use a diode based isolator with an alternator
But you can not use one with a solar controller
The controller must be connected directly to the batteries
You could install a switch between banks or use them all together
Which is what most of us with enlarged Battery banks do
I do have a power connector which lets me unplug one bank then charge it sperately using a battery charger
Most of us have separate house and chassis systems, But leave all the extra batteries for the RV house system connected together