I'd consider leaving the alternators as they are for now. Just make sure that each has a good independant Negative to Engine block, and that the charge leads are sized appropriately.
Is the boat now set up with an MBSS.... (main battery selector switch)? Or a pair of MBSS's?
Typically, until we get up into larger boats, our Stbd engine alternator, and 2nd Battery Bank, will serve as the House Load Battery Bank and charging system.
If you wish to bring in the Port engine alternator, consider a Bluesea ACR or a VSR to do the engine alternator combining automatically for you.
This way you will not need to separate your system out, and yet it will maintain your redundancy re; ability to combine, should you need to.
Bellow is a very basic, yet very dependable twin engine battery scenario that uses two MBSS's.
This still requires manual battery management, but for many of us, this is not an issue!
This also gives you the option of a Stbd side cranking battery (not shown) if you want to.
( I crank my Stbd engine on a large House Load Battery Bank.... no issues to date)
Note the option for a helm switch activated "Solenoid Combining Switch" (for engine cranking..... not alternator charging).
IMO, combining should be reserved for emergency use..... not necessarily charging unlike battery banks.
You can add an ACR/VSR to this.
This is simply a suggestion, as there are many ways to skin the cat.... some better than others.
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