So let's see how this works...
DT, when running, switch the genset batt to "both". This will allow the port motor to charge the genset batt. When you shut down, switch the genset batt to "1". In fact, you may not need the isolator. Anyway, house loads and genset starting are on batt 1 of the genset switch, if you run down that batt, switch over to "both", and that will parallel the port batt with the genset batt.
I forgot to say, when starting, starboard batt switch is on 1, port batt switch on 2.