I thought alternators did not like charging depleted deep cycle batteries? Is this an old wives' tale? Great info on this thread BTW.

I only run deep cycle batterys on the boat. and never had a problem.

not a problem for the alternator it will just take longer to charge two back up, but if you plug in when you get back to the dock that is irrelevant.

never had a problem either, the only alternator problems I had were from Eliminators ****ty rigging job pointing the air intakes right at the starboard alternator which here in the salt water meant if got a spray of salt everytime we went out, so I had to rebuild it yearly, the port never had an issue.

Yea I am not worried about it dieing really, as it sits now with only one house battery I am ok, and only SOMETIMES run it low enouhg that motor wont start. But I have genny and charger, and the whole extra battery and motor. i just want to make the house/port motor have extra capasity.

Sorry it seems foreign.
First consider the battery bank is depleted. He runs one large Kinetik but duals have similar or more capacity.
When batteries are allowed to run down to 11.5v and the HU/amps start to reset; 50% battery capacity or roughly 100a/hr depleted. The charger will do everything it can to push charging voltage to 14.5ish. It is also trying to monitor this state to provide an appropriate charge profile.
If the stereo continues to exert a load, in this case 50a+ transient (90a fuses) it is more than the charger can do to even keep up, let alone charge. Internal components WILL fail.
Using relatively low amperage, consistent pulls on charged batteries will take a long time, if ever hurt the charger. Starting the genny/charger at the beginning of the day will help relieve demand as for much of the time the batteries will at least remain charged but the constant fluxuation and negative net power will eventually damage a standard charger too.
As I stated however, many people wait til the batteries start getting low, then kick on charger while amped stereo is pushing hard (again late day usually = louder play).
This WILL damage a charger.

A power supply is built to identify the difference between charging profile and supplying power to the battery. It will say "hey, I can only give 12.9v based on draw so I will not even try 14.5". When the draw is reduced it will recharge the battery bank but will not go into full profile charge mode til is senses the major draw has stopped.
This does not mean you still might not trip a power supply but with a larger one and connected to batteries, this is highly unlikely.

Alt does not know the difference between deep cycle or any other type.

Good reading, as are the other 6 parts that would cover many other questions - http://www.bdbatteries.com/autosizing6.php

A larger battery bank will put excessive draw on the alternator if the battery bank has been depleted.
With average boat use this problem is compounded by two things. First, alt output is a function of rpm. Thus to achieve 90amps, the engine must be turning at least 3000rpm for example.
When you first fire up and idle to warm engine and leave cove for instance, alt is probably only putting out 1/3 that amperage, but it is still trying to push up to 14.4 volts. If the stereo still cranking as the party continues. this compounds the situation by placing further demand on limited output.

Alt will burn up its regulator or other diodes if there is too much difference in output vs draw. This is why in car audio, you see them adding huge 150-300a alternators.
Boats don't necessarily have to do this since much of their heavy output is with engines off but if motor is running, alt capacity needs to be factored. Many can get by bumping from a standard 70a alt to 110a and relieve the problem.

Boy, there is a lot of misinformation on this thread.

I have been rebuilding, repairing, and selling, starters, alternators, and batteries for about 35 years. I have retro fitted, designed and installed more charging, starting systems on boats, planes, cars, and trucks, than I can remember.

Following is a description of my system that I installed several years ago in my 42 Harley.

Boat has twin engines, a gen, four battery banks, and an on board charger/inverter. I use battery combiners between all banks with simple on-off battery switches for each bank. I also have one parallel bat switch between the two starting batteries, just in case. It is left in the off position under normal circumstances.

When the boat is plugged in to shore power, it will charge all four banks via the combiners, when one or both engines are running, it will charge all four banks via the combiners. When I am at anchor, I can start the gen and it will do the same. I frequently run the gen while under way, so the on board charger is operating, and both alternators are charging with no problems. Neither the alternators nor the on board charger will be harmed if ran at the same time.

Battery combiners when activated combine two battery banks in parallel. I stopped using isolators many years ago because they can ruin your alternator if they fail with an open circuit. They are also harder to install. Combiners are easier to install, and if they do fail in the open or closed condition, the worst that can happen is a dead battery.

I do agree that you should keep all of your batteries the same age if you can, but it's not the end of the world if you don't.

I have installed dual alternators on several applications. They do not have to be special, computer controlled, or a matched set, just hook them up and go.

I have never had a problem running multiple alternators to one battery bank. I have seen many problems with multiple batteries paralleled into one bank and sitting idle (not being charged or discharged).

It is true that the alternator generating the higher voltage will carry most, if not all the load. If the recharge current were more than a single alternator could live with - say a very large and very depleted bank - that alternator carrying the greater load could overheat. But the fact that a second alternator was also feeding into the bank would not make it work any harder.

Ideally I would have two banks, one for starting and essential loads and the other for a house bank. Use a 2 bank switch for each engine. Leave one engine and the generator on the starting bank and the other engine on the house bank. If the house battery is too discharged to start its engine, simply switch to the other battery. After all engines are started, switch one engine through "all" back to "house" to recharge the house bank. As already mentioned, using an automatic battery combining relay simplifies the process.

Never switch a working alternator to "off". The spike can kill it. But unless an alternator or regulator already has a problem (or there are other wiring issues, like a poor ground) it shouldn't hurt to combine them.