First of all, I'm no expert, but... within that... I think a lot depends on how you plan to use the boat, and how you plan to keep the boat when you are not using it.
Examples of what I'm thinking:
Two use cases that would put very different loads on the house bank:
1) Run out fishing for a day, motor(s) are on much of the time, run back.
2) Motor for a few hours to an anchorage and then spend two days living on the hook.
Storage:
1) Kept on a trailer at home, with a shore power "hookup" right there.
2) Kept on a mooring, with no "plug in" available.
You can probably see how the above "extreme" situations would call for different set-ups. Use scenario one puts very little strain on the house battery(s), and in addition the engines are charging them pretty much constantly. Scenario two will put much more of a strain on the house bank, as you motor very little (thus charge very little) and then try to "live" on the house bank over a period of days.
Storage scenario one is also different from scenario two.
From what I have learned the "simple, basic" setup (and that's not to say it's a bad or even lesser choice at all) is two identical deep cycle batteries, often Group 24, with a switch between them, and you just pick one for starting and one for house and then you can alternate days if you want to. You may have a bit "less" battery than you could have for house, and a bit more than you need for start, but it's perfectly adequate in many situations, and simple.
A more "cruising boat" setup may be to have a dedicated start battery (which can be smaller but still needs to be adequate) and then a larger, dedicated house battery. This would be lend itself more to a scenario two type of setup.
You can add a VSR (such as Blue Sea ACR or other brand).
One thing to keep in mind is how many amps your engine puts out (alternator), how long you plan to motor as opposed to using juice, and what other (if any) sources you have to "put back" amp hours (shore power, generator, solar panel, etc.) It's good to keep a balance. For example, if you are relying solely on the engine alternator to charge the batteries, you don't want to have a huge bank (many amp hours), run it way down, and then have to motor 27 hours to bring it back up.
Another consideration when planning amp hour usage is that you don't want to run batteries down below 50% charge if you can help it - it kills them much faster. So if you have an 80 amp hour battery, that's really 40 (or so) you want to use.
My boat came with the typical setup (two group 24 batteries and a manual "Off-1-2-Both" switch. I'm sure it would have worked fine, but since the batteries were old and dead, and since I hope to have cruising scenario two, I went with a smaller, dedicated start battery, and a deep cycle Group 31 house battery (only very slightly physically larger than a Group 27, but more amp hours). I put in a VSR and an "On/Off (combine)" switch. I don't have a charger (yet), but may add one.
I went with AGM batteries, because the way my house battery is situated it would have been hard to check/fill water level on a flooded cell battery. As it turns out, I also mounted the start battery on its side, for more efficient space usage (you can do that with AGM's).
Upshot seems to be that many systems will work, and some may be slightly better for various specific use-case scenarios.
Sunbeam