I'm sure it would help greatly if I understood any of it.... Def
With all respect I would disagree completely, too big an alternater could adversely affect the batteries. A cranking battery will accept charge at a different rate to a deep cycle battery (cranking tend to be more forgiving), and if you try to "force feed" them you'll just hurt them. As for the isolator I would recommend a split charge relay, as there's no worries then about forgetting to turn it on when charging and off to avoid transfer to the cranking battery. A bigger alternator would just mean that heavier cables, connections, fusing and relays are required ... as well as the battery issues. There's just no benefit in simply going for the biggest possible IMHO.