i'm not sure why you think you need an isolator in the first place. if all you have is a starting bank and a house bank charged with a dc/dc charger, why bother?
take the alternator direct to the starting bank and let the dc charger do it's thing charging the house bank. the dc charger should have diode protection to prevent current flowing the wrong direction. some sort of manual switch to isolate the house bank is probably a good idea, but an isolator seems unnecessary unless the dc charger specifically requires it. if that were the case an acr might be a better choice.
take the alternator direct to the starting bank and let the dc charger do it's thing charging the house bank. the dc charger should have diode protection to prevent current flowing the wrong direction. some sort of manual switch to isolate the house bank is probably a good idea, but an isolator seems unnecessary unless the dc charger specifically requires it. if that were the case an acr might be a better choice.