Sky, we changed the battery setup on my boat at the same time as we made some other changes, specifically:
-dedicated starting bank
-dedicated house bank (deep cycle batteries and much larger)
-dedicated starting battery for generator set
-smart regulators operating alternators, both regulators made by Balmar
-we kept the paralleling switch in the system
-smart high-freq charger (a StatPower, although if I were doing it now, I would get a Victron based on Scott's experience with them)
The original system had two 8Ds, one ahead of each engine, and split up the house loads between them. The marine electrician who did the work pointed out that having the house loads split up increased the chances of running both batteries down to the point where they couldn't start the engines (which had indeed happened, although I don't recall the circumstances) We ended up with two Group 24s in parallel as the starting bank, one Group 24 as the generator set starting battery, and two 4Ds as the dedicated house bank.
This has worked out well. The original starting batteries, the two Gr 24s, lasted eleven years- about two or three times what I expected. I have thought about adding an inverter, to run off the house bank, but unless and until I start anchoring out, which I don't do right now, I probably will not buy one.
Some of the changes I made were in anticipation of uses which turned out not to happen (I may not be the only one here who's done that) What I CAN tell you is that (fingers crossed) I have not had to confront a no-start situation since we made all these updates, and I am happy with them. I wondered whether two Gr 24s in parallel would be a large enough starting bank, but they have done fine.
I forgot to add that each engine's alternator charges one bank- the smarter of the two regulators is on the house bank.
I suppose the underlying theory here is that starting batteries and deep-cycle batteries differ enough that the tasks should be separated, if that makes sense.
The one thing I am sorry about is that I took the Hatteras battery case out of the stbd side of the engine room. I should have left it in there. I had to destroy it to remove it, and it was stupid to do so. If I could find another one, I'd put it back in, for storage. They are very well made.