Isolators are pretty much old school technology today. A better product would be an ACR (auto charge relay) or a VSR (voltage sensing relay).
But let's back up for just a minute.
Your 1-2 both battery switch can be thought of as an MBSS.... (main battery selector switch).
If your single engine boat is set up correctly with the Engine Harness including the Alternator charge circuit, this alternator charge circuit will be a direct connection to the MBSS "Common" cable (generally terminating at the starter motor solenoid).
This means that whichever battery bank has been selected, it will be supplying ALL 12 v power and will be receiving alternator charge.
Now if you want to add an ACR/VSR, this divides the charge between the two banks regardless of MBSS selection.
When the MBSS is managed correctly, most owners will crank on Bank #1 (a dedicated cranking battery) and will warm engine. This bank will be charging while warming engine.
Then switch over to #2 (a bank of Deep Cycle batteries) and use accordingly, keeping #1 in Reserve until cranking again!
(key point is in keeping #1 in reserve)
There are a number of ways to configure a dual battery bank scenario.
I suggest
KIS.... keep it simple on smaller single engine boats!
Here is a very simple schematic that is both KIS and yet works well for manual battery management.
Note the Un-Interruptible bilge pump "float switch" circuit, and note the direct O/B Charger-to-MBSS connections.
(schematically the same.... but with no Rat's Nest at batteries)
The New House circuit and panel is optional, but not a bad idea, especially if you start adding GPS, DS, FF, etc. This takes the OEM hull harness out of the loop.
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