I think the problem is that to charge two large batteries, you'd need a pretty large solar panel (or panels); you can get small 1 to 5 watt panels, but they will just serve as trickle chargers and probably won't do much for batteries that have been discharged.
If you go with larger solar panel, you probably will need to look into a solar controller, which would direct and control the charge to your battery bank. I would think that using the Noco charger would require you have in inverter to produce 110v power; probably easier to have the solar panel controller charge the batteries.
There have been quite a few discussions on this in the past, and outside of a trickle charge to maintain batteries while you're away, it seems the consensus is that solar panels to charge depleted batteries aren't that practical due to the size of panel needed.
He will just have to get a bigger boat to support those bigger solar panels!
Good excuse to go bigger!
All kidding aside, if you're just looking to maintain the charge of the batteries, it should be ok. But if you're looking to actually charge a depleted deep cycle battery for trolling, then you'll need a much larger setup.
Just wondering why you would need an external charger. If you're just looking to charge your starting batteries, doesn't your engine do that?
You can add an ACR so that your engine will keep both batteries topped off automatically while it's running. Or you could just add a battery switch and do it manually by switching to 1,2 or both.
I trailer my boat now, but I never have to charge either of my batteries. The engine does that when I use the boat.
If I had a trolling motor powered by a deep cycle battery, then I'd have to use an external charger for that after each use.
The only load I have connected directly to the battery is my bilge pump. It is always energized regardless of the battery switch position.
When I used to slip my boat, I would turn the battery switch to off, but my bilge pump will operate if needed. Will the bilge pump kill the battery? If your boat takes on enough water, probably and I don't think a solar charger would keep up with that.