Batteries
HTR,
Ok, first -- Battery Technology: Gel and AGM batteries have a tighter tolerance for charging voltages than do traditional flooded wet-cell batteries. The reason for this is because during the charging process, all lead-acid batteries off-gas (hydrogen ions are released for the acid solution, causing the boiling point of the liquid to be lowered, causing the water to boil, releasing the now dissolved hydrogen gas and water vapor), i.e. some of the liquid electrolyte is evaporated out of the cells due to the inherent temperature rise associated with the Bulk phase of the charging cycle. The amount of off-gasing is directly proprtional to the bulk chargin voltage, so a higher voltage will result in more heat and more electrolyte lost. In traditional flooded batteries, this is visible by the fluid level in the cells dropping, which is why periodic maintenance on these batteries is necessary to ensure proper life-cycle ("topping off" with distilled water). in el cell and AGM batteries, there is significantly less electrolyte to begin with, and the cells are sealed, preventing the owner from adding fluid. The evaporated electrolyte appears as a white powder on the top surface of the battery. If the plates in the battery are allowed to become exposed, then the battery is headed for a quick and permanent death. Therefore, in order to reduce the potential for electrolyte being lost through off-gassing, the charging votlage for AGM and Gel batteries needs to be tightly controlled at a somewhat lower voltage than traditional flooded cell batteries (13.9-14.1 vdc vs 14.1-14.8 vdc). How does this affect what your Yamaha guy told you? Well, if the alternators Yamaha has installed do not have sufficient tolerance on the voltage regulator, then the added cost of sealed battery technology is wasted due to the shorter life span those batteries will have. (Typical life-span for Flooded-cell batteries properly maintained is 3-5 years, Gel cells with proper maintenance (charging & use) 4-6 yrs, and AGM batteries (again with proper use and maintenance) is 5+ yrs.) With improper chargin, I have seen customers with AGM batteries return within the first year (they were using a charger with a typical output over 14.6 vdc).
Now, lets talk about the different duty ratings. Walk into any marine supply store and you will typicaly see three type of batteries. Starting (or Cranking), Dual-Purpose, and Deep Cycle. Starting batteries are do what their name implies -- Start engines. They are designed to fill this role by using a high quantity of thin plates in each cell, allowing the electrons to flow rapidly out of the plate and into the electrical circuit. This design also has the advantage of being able to allow for multiple starting attempts in a relatively short time-span, since the thin plate design also reduces the amount of time needed for the battery to "recover" (new electrons to flow to the plate surface) after a starting attempt. Starting batteries are most similar to automotive batteries, and can be deeply discharged (up to 80%) without long-term damage to the battery.
Dual Purpose batteries also are contructed to perfom as the name suggests. These are kind of the "Jack of all trades - master of none" of marine batteries. The have fewer thicker plates than a starting battery, but not as thick as a deep cycle battery would. This allows them to still perform the cranking function adequately without risking damage to the battery, but the thicker plate also allows for a slower release of electrons into the electrolyte, which enables the batteries to supply electricity for long-term low current loads (cycling).
If Starting batteries are thouroughbreds, then Deep Cycles are clydesdales. These thing are beasts, constructed of a relatively small number (sometimes as few as 2 per cell, 1 positive and 1 negative) of thick lead plates. These plates can handle the high-discharge need of cranking, but only in an emergency for a few attempts spaced well apart. The electrons are released slowly from the plates, making them ideally suited only for connection to steady-draw, low current loads. These batteries' life spans will be significantly shoirtned if discharged below 50% capacity, due to the enormous amount of time needed to re-intorduce electrons to the plates. Typically, these batteries will exhibit the longest life span if kept no lower than 80% and allowed to charge on a prpoper charger for at least 8 hours.
So, How does this help you? Well, if you are hooking the two batteries to the smae electrical circuit, then dual-purpose is the way to go. If you are going to have a dedicated starting circuit, then I would recommend a High-capacity starting battery (1000 MCA) and an isolated deep cycle batery to run your cycling loads. I would also have these two batteries connected via a paralleling switch so that the Deep Cycle battery can augment the starting battery in an emergency. (such a switch would remain "Off" under normal operating conditions). As for battery technology, I would choose traditional flooded lead-acid batteries. You will have to periodically check and top-off the water level, but for the life span vs cost equation, on outboard-powered boats, they are really the most cost-effective. If you aren't the type of guy that is religious about battery maintenance, that's fine, just be prepared for a maximum three-year life span. This makes even more sense when you figure that a wide-tolerance alternator output can reasonably be expected to give you three years out of a gel or AGM battery as well, at a higher cost. If you are set on sealed battery technology, then definitely choose AGM, as the performance with that tech is vastly superior to the performance of Gel-Cell, and contact a reputable Yamaha engine center to get detailed specifications on the alternator output for your particular model engine.
Hope this Helps!