Hi BruceK,
I like that idea! There would be real value in adding a panel or two so I could float the start batteries separate from the house batteries.
But, I always try to look at my flavor of boating before doing things like that. In reality, don't really leave the boat that long without having AC power, either from the genset or shorepower. When I'm cruising I usually run the genset for 30-45 min nightly, usually while cooking -- it puts a load on it, makes dinner, heats the hot water back up, and tops off the batteries. Maybe heats/cools/dehumidifies the boat a bit.
Given where I am now with this boat, and how I tend to boat, the most impactful electrical change I could make for me would probably be to go from 2x4D house batteries to 4x4D (or equivalent) house batteries. I'd love to be a sailboater one day, both in boat and boating style. But, for now, well, I've got plenty of diesel aboard to burn. I'd have added those batteries already, but I'm still learning where I want them based upon where I tend to crawl to reach things, etc.
In my last boat, I didn't have solar power at all. Between the shore and the genset, I was basically set. I always wanted it "in case" I ever left it for an extended time at a mooring -- but that was never the case.
When I bought this boat, I upgraded some things to meet the way I used the boat, e.g. added a bigger charger and an inverter/charger; fixed some things to be more code compliant, e.g. added battery boxes (moving things to make room), protected all loads, etc; and reorganized things to better suit my use.
With respect to the reorganization, the boat seemed to "originally" have 2x4d batteries for each engine and 2x4D batteries shared by the generator windlass, and house, with the PV system tied to the gen/house/windlass. But, by the time I got the boat, one house/genset/windlass battery had been removed -- and the other had blown up, because the PV controller was set up to charge at 14.7V in all modes, e.g. float (guess = that's what happened to the removed house battery).
As I mentioned, I was going to add more batteries. But, I just couldn't get happy with where to put them. Just by adding the battery boxes space got impossibly tight and I had to relocate the genset battery from where it had been (near house and engine start batteries) to its present location (aft of generator).
At any rate, I've got two large PV panels right now, wired in parallel, and going to a single controller. Eventually, I may look at separating them and adding a controller so I could, as you suggest, have one panel for house and the other for engines. Maybe I could add a panel -- but that would likely involve sacrificing space I want for something else.
I feel like it is more likely that I'd just add a small flexible panel in the little bit of space I have above the bimini to float charge (and only float charge) the start batteries, leaving the big one to handle the house+windlass, and only the house+windlass.
But, even that is pretty distant priority. There are so many other project on my list before that, from upgrading electronics to new carpeting to adding an oven, to putting the controls which had been removed back on the lower helm, to putting on some doors that had been taken down, to...
...guess that's why they call it a priority list
Cheers!
-Greg