I am redoing mine as well and have a similar setup. You can use a single
isolator and then tweak the regulator
voltage so you compensate the voltage drop.
They make cute gadgets (auto charge relays) that tend the starting battery and then you don't need an isolator. The one on mine was an Ample Power
Eliminator. On paper they sound great and original owner of the the boat said it worked great - but it died between when he sold it and I got it. That is how my mess came to me after the most recent owner got the boat from a yard or did it himself. They can still bite you when you get into other situations too so in the end you are stuck with some scenario that can end run the plan. Personally staring batteries are cheaper and as long as anything is running I can start the engine
You can attach the shore power charger
directly to each bank (starter and house) The Xantrex supports an equalization
cycle so you can take the 4 golf carts and make one bank. It's easier to do that. So on shore you have what you need all the time for each.
What I did with the switches is this. I have two (1,2,Both, or Off) switches. The first is used to put all 4 golf carts in a two banks but combined when in the (both) position. Now if I notice one of the batteries is acting funny
in a cell or two I can switch that pair out (switch to 1 or 2) of the setup and not have the bad cell cascade to the good pair. That was always the reason you made separate banks of flood batteries. I can use the OFF position to just shut it all off so I can work on it (the solar
panel is always on in the daylight).
The second switch is set to 1 so the starter battery starts the engine. Position 2 would let the house bank start the engine and both would maybe never be needed but if it came down to it everything can be used.
I also have a battery monitor
on the two banks. The only hole is that the alternator regulator
is based on the house bank sensor and the starter goes along on the same ride with the isolator. For about $400 you can get something to handle that instead of a $70 isolator. There are products from Balmer and others. Read all the details before you jump on board.
My solar panels
are handled by the same regulator that handles the alternator so that input is properly regulated. The House bank has it's own shore charger regulation and so does the starter.
This all works pretty well since you never need to turn any switch under normal operations. You don't need to remember what to switch is off or on unless it's not normal.
You could stay with three banks but then you end up spending more money
and have to remember to alternate the house banks regularly. Since you need to watch flood batteries any way if you can switch out a bad batter at least you have 1/2 capacity and that is all you could ever have in a three bank situation. If you let the bad cell cascade then you were not watching close enough any way and it's the same damage.
My last boat was set up similarly except with AGM's as the house bank. This setup is tuned more for flood batteries and since the regulator is a nice one and I have a spare brand new one it seemed a better choice than switching all the gear
to handle AGM's (really are better).