The heart of a sailboat's electrical system is its batteries. Keeping in mind issues of weight, space, and location, it makes sense to get the biggest bank of batteries you can fit on your boat. Regardless of your expected daily load, the larger your bank of batteries, the less deeply they will be discharged, and the longer they will accept high levels of charging. There is no good reason to divide your house batteries into two banks--not only will this complicate your wiring, it actually increases the wear on individual batteries and makes charging less efficient.
You don't need to get the most expensive batteries out there. On our old 28' Triton we had two expensive AGM batteries and spent plenty of time in the dark (for which, however, I can only blame our naive faith that solar panels alone would get us through Fall on the Chesapeake Bay); on Momo we use eight Trojan 105's, which are standard flooded 6-volt golf cart batteries, and we've never had a problem. Theoretically, this bank yields 860 amp-hours. Nothing did more to convince us about the virtues of the Trojan 105 than watching it in action. In Ensenada we shared an anchorage with friends who were rebuilding their 120' ferro-cement ketch. Using arc welders, drill presses, table saws and other heavy equipment, they subjected their bank of Trojans to an abuse much more intense than any cruising sailboat could ever deliver, torturing their batteries to the brink of death almost every single day; and they always recovered.
Newer battery technologies, like Gel or AGM, might very well be "better": they accept larger charging levels and deliver more power faster; they also have a lower rate of self-discharge than flooded batteries, although this does not matter if you're actually using your batteries every day. Building a bank with Gel or AGM batteries, however, costs more than twice as much as with flooded batteries; and the larger your bank of batteries, the less significant are the advantages offered by newer battery technologies. Your engine might very well start better using a single AGM battery than a single flooded battery. But if you have eight batteries, who cares? Likewise, you may be able to charge a single AGM battery more quickly than a single flooded battery. But the equipment needed to attain a similar degree of charging efficiency on a large bank of batteries is more than we can afford anyway. In any event, if you need to make a choice, it is better to have more amp hours using flooded batteries than fewer amp hours using Gel or AGM batteries.
In two important respects, newer battery technologies are actually at a disadvantage when compared to their flooded counterparts. The first is that, because they are sealed, Gel and AGM batteries can't tolerate being overcharged. If your system starts overcharging your expensive high-performance Gel or AGM beauties, it will toast them. In contrast, flooded batteries require periodic over-charging as part of their regular maintenance. During this process, called equalization, they vent off explosive gases -- a fact which scares some people. But since these gases are lighter than air, as long your battery boxes are ventilated, they will dissipate. Moreover, if your bank of batteries is large enough, I doubt your charging system will ever bring them to a vigorous boil. Ours most certainly cannot. A second advantage that a battery like the Trojan 105 enjoys over its more sophisticated competitors is that people play golf all over the world, and they need golf carts. Thus, if you ever need to replace your batteries outside the USA, it will be much easier to find something that fits your boxes than if you used batteries with more exotic dimensions. Keep this in mind, too, if you're considering those most aristocratic of flooded batteries produced by Rolls-Surrette.
Sure, newer battery technologies--especially AGM--have plenty of enthusiastic proponents. But before buying those vaunted AGM batteries, which were designed to withstand the G-forces of military aviation, ask yourself how frequently you'll be sailing your boat upside-down. Keep in mind, too, that even if you take care of them, AGM batteries don't last any longer than flooded batteries. A friend bought a brand-spanking new Nordhavn just after we bought our Trojan batteries (2005). He had to replace his AGMs last November (2009), while our Trojans are still going strong. I know for certain that he has a much "better" charging regimen and puts a lot less strain on his batteries. He also likens owning a boat to "ripping up $100 bills in the shower, just quicker." I can sympathize with him, but I'm grateful that our experience had been different (especially since we don't have very many $100 bills).
