I have heard conflicting stories as to if you have your dual battery switch on or off while running the boat! I believe Formula says to have it on to charge both batteries, but if both motors are running with 1 and 2 on are they not being individually charged??

Its going to depend on how the Mfg wired it, but....if each switch is dedicated to one motor then it should hold true that on position 1, each motor "should" be charging its own dedicated battery.....so when running each switch should be on position 1
You would only need to switch to postion two incase that motors primary battery was dead...or switch to BOTH if you know the other motors alternator has crapped out so both batteries are getting charged. If both motors are running properly (alternator wise) you dont want to run the switches on "Both" as the alternators will be fighting each other.
Also never switch then OFF with motors running...you can damage the alternator as well...

Wally wouldn't it just give you twice the current if you are running in both? It is DC so it should not matter I think.

Running on both can cook a battery if your batteries are discharged at different levels. Once you have both engines started you should switch them back to their own battery so you draw the right amount of current for the state your battery is in.

Sort of, but not really....the alt can only supply so much current ...So lets say they are rated at 105A ea.....thing is, most times they only produce what is required of them.....So if the load on the alt at the time is only 10a then that's all it will make.....the issues pop up when you have one alt that's stronger then the other (and there will always be one since you wont be able to perfectly match them up) and that one will back feed the weaker one and eventually crap out the voltage regulator/rectifier and pop goes the weasel!


Think of it like this:
You have two water tanks....one is 500 gallons and is 10' tall.....the other is also 500 gallons but is 15' tall....both have the same size opening at the bottom and you just hooked them up onto the same hose. When you switch the valve open on the one tank you get 10 gallons per minute....when you switch it to the other tank it give you the same 10gpm.....when you open both valves you will still get the same 10gpm but if you watch the tank level in the shorter one, you will eventually see it start to raise as the water pressure in the taller tank will back feed into the shorter tank and level them both out. Now this example is very crude because those in the hydraulic world will know there more involved here but i was just trying to convey a point here.

Bingo! Only use the combiner switch when you HAVE to.