Not sure what you want to do: Yes a charger will charge 2 battery banks with the isolator or just a switch between the batteries and there are many ways to do this.
But since you want to charge with the charger then you already have 120V so why did you let the batteries run down?
If you are boon docking and run down the 6's just switch over to the fresh 12V battery and bring in the slides. But a isolator or switch connecting the 2 banks may not work because the discharged 6's will start pulling some power from the 12's. It all depends upon the batteries capacity, SOC and how much power the slides draw. Typically the slides can require a large amp draw and you may not have enough voltage from the connected battery banks.
You could setup the situation you want and try it and see if it works.