All of your house batteries should always be hooked up together. The chassis battery (ies) will be on a separate circuit and may or may not be charged by the inverter/charger.
I assume you have 4 6V batteries is you have a bank of 4. 2 will need to be connected in series to create a 12V circuit and then the 2 12V circuits will need to be connect in parallel to increase the capacity without creating a 24V circuit. There are some easy to understand diagrams here but there are many good instructional information out there.
Batteries/serial/parallel