What if I already have a large 12V battery bank, inverter, solar and it’s working pretty well. Can I replace my 180 amp alternator with this system? So I would have a small 48V bank and a large 800-1000AH 12V bank. Also will my 12 volt bank be charged by solar and my inverter (when on shore power or gen.) be able to charge the 48V bank?

You would want to reconfigure the batteries to maximize the 48V bank, as this will optimize the charge acceptance rate and reduce battery-charging times. You would then have a small 12V ‘buffer’ bank, maintained in a full state of charge by a Integrel 48V to 12V battery-to-battery charger. Your 12V inverter/charger will not charge the 48V bank so you will either need a stand-alone 48V charger, or a 48V inverter/charger, both of which Integrel can supply.