Can you charge them both simultaneously from the alternator? You know, the battery switch. 1, 2 or both? https://www.cpperformance.com/p-8027...4-pos-afd.aspx

Yes, I have a battery switch for each engine. Position 1 is the starting battery for each engine. The deep cycle is wired to position 2 on both of the Perko switches. I can turn either Perko switch to ALL and it charges that engines battery and the deep cycle at the same time. If I switch both of the switches to ALL, it combines all 3 batteries, so theoretically, as long as I have one good battery I can start both engines. I have never had to do this and I never run the boat with both of the switches on ALL.

Throwing this out there, but there are a ton of great Chinese lithium batteries on Amazon. Fraction of the weight, about the same price, and will last you much much longer than standard lead or AGM

Only issue is you may need a DC to DC charger depending on your alternator

All batteries are made by one of 3 manufacturers, X2 is most likely the best you will find, better than optima and odyssey as they are both declining

I’ve looked into the lithiums and also AGM. I’m not really interested in the lithium right now for a few reasons. The AGM seems like a good choice, however I know they’re sensitive to high voltage charging. I have twin 500EFI’s with stock alternators and have seen the voltage gauges up to just under 15V before so I’m a little concerned I’ll get boil off of the electrolyte.

I appreciate everyone’s feedback so far, thank you!

I don't think you can do better than the dual-purpose AGMs from West Marine. I get 6 years minimum from them, regardless of what they're asked to do. But, they're not cheap.
As a bonus the AGMs are a lot less sensitive to shock and vibration damage. I've tried. I switched to AGMs exclusively years ago after experiencing internal breakage on a few wet cell Interstate starting batteries (1000MCA) after hitting wakes.
My wife was stranded just last summer from a wet cell breaking internally on her 2023 jet ski. The higher the MCA rating the more likely that happens due to the thin plates.

As mentioned above I would highly recommend the 3 position switch route. I run two deep cycles in my boat and they crank a big block just fine. Also installed a min Kota in board charger with a flip up cover so I can easily plug the charger in without having to get in the boat.