Lets first discuss how some two engine boats come wired from the manufacture.
With out getting to techinical at this point, this is what I have found.
They use one battery to start both engines. Makes sense as a person would not normall try to start both engines at the same time.
Usually this battery is connected to the port engine. It is usually switched on and off with a simple on/off MBSS. When on it provides all the power that is needed for running the boat. The house circuits are usually tied to this battery if only one battery is used.
If only one battery is shipped with the boat, the boat has the following wiring
The second engine (usually the starboard) is wired with a sense wire from the alternator
to a battery. The charge (output) of the alternator
is also wired to this battery.
So if there isn't a second battery the alternator is disable because the sense wire has no volteage.
If a battery is present a simple on/off MBSS is used to provide power to the house circuits. House circuits are any circuits not required when the engine(s) are running.
Some manufactures will provide another on/off MBSS that can connect the two batteries together for emergency
starting. The con is if this switch is left on without the engines running or a charger
hooked to the batteries, it is possible to drain both batteries with house loads.
The above does work and many boats are wired that way.
Another was is to have both engines wired the same. Makes it easier to trouble shoot.
In this case a 2-4 position (Off,1,2,Both) MBSS is used. Both engines are wired the same. The common is connected to the starter of the port engine. 1 to the first (port) start battery, 2 to the first (port) house battery.
The starboard engine would be wired with the common going to the starter, 1 to the second (starboard) battery, 2 to the second (starboard) house battery. The sense lead has to be connected to the house battery
It's a good practice to add another 4 position MBSS. Common goes to the house loads/battery charger
. 1 goes to the port house (at the port switch) and 2 goes to the starboard house (at the starboard switch).
IMHO this gives the best for ballancing the alternator output. Gives you the ability to isolate batteries. If you have two batteries in parallel and you loose a cell, both batteries will go bad if left connected. If you loose an alternator you can use the switches to charge all batteries.
There are ways to use on/off switches and automatic charge relays (ACR) for less switching.
Using a 100 amp alternator to charge two group 27 batteries is way over kill.
Two group 27 100 amphour batteries is not very much. First if you discharge more than 50% you will shorten the life of the battery. The majority shoots for 40% discharge. so that would give you only 80 amphouse of usefull power before having to charge your batteries.
I have a 32 foot bayliner. The biggest drain is the refer. Next would be the water
pump. How late you stay up governs your light usage. We end up using about 60 amphouse a day. So the group 27 would last us about a day.
The conses is golf cart batteries give the best bang for the buck. We have 4 golf cart batteries in two banks. Gives us an easy three days until we have to charge the batteries.
The above should give you plenty to ponder.
Ask away if you have any questions.