I have two batteries in my boat now on a perko switch. Im thinking about upgrading my stereo again with another amp and more speakers. So Im going to need another battery. I was going to run two batteries in series for the radio, and just one for the boat itself. So how many batteries can I safely charge off my factory altenator? Its a 96 502, so I believe it has the 80 amp??

In series - you'll get 24vdc from two 12vdc batteries. Yes, you can charge two 12vdc batteries in parallel with your alternator.

Sorry I mean I will be running them in parallel...positive to positive, negative to negative..So will I be able to charge in theroy 3 batteries off this alt with no issues..

i don't see a problem. unless they are all 3 so dead they won't start the motor, the draw won't be that high. and if they are all dead, the alt won't charge anything...

A simple way to view you issue is this.....

The alt is a faucet. The batteries are a tub. The faucet has a set output.....let's say 1gallon per minute.

Your batteries are the tub.

If you are doing well with a faucet that fills your tub at a rate of one gallon per minute, but add an additional drain ( stereo) you will see that the faucet is no longer able to keep up with the additional negative flow (consumption) and the first and worst thought is to add another battery (tub). In doing so, you have actually made the problem worse. The struggling alternator has a higher demand with 30% more "tub" to fill.

By adding a 3rd battery AND upgrading the stereo, you have actually gone backwards in the attempt to maintain a 12.5 reserve start/engine and a 12.5 reserve house (minimum)

You will soon find that a bigger tub is good......but without a bigger faucet.....you will begin to hate your entire electrical system. Lights dimming and radio shutting off when bass notes take a long hit, windlass tripping the breaker (if you have one)...misfiring if you have upgraded ignition..(msd).....

I have two engine/start and 4 house running ac, lighting and 6k watts........both engines have dual out 130a alt. One side to house, one to engine. Never an issue....

The bathtub analogy is good but an alternator can still burn up attempting to reach its desired voltage with too much draw from any combination of depleted batteries and system draw.

Adding two additional batteries to the house bank should not be a burden. Just don't run the batteries down, start the motor and expect to keep playing the stereo. These actions, especially at low idle will destroy alts.
Make sure you are plugging in with a charger to fully charge at the end of the day. An alt will not be able to fully recharge batteries most of the time which will lead to disappointing performance and shorten battery life.

I would suggest adding an isolator between the two sets. One side is start, the other for house and radio. This setp allows the radio, fridge, etc from the house to run the batteries down without effecting the start battery. Fire it back up and recharge the house. Along with this setup I also have a dual battery charger. Has work great for years

I dont have a frig or anything like that.... Run the radio off two batteries in parrallel...and run the motor/k-planes/and rest of the boat eletronics off another battery. And they are on a perko switch..The radio/amp is directly connected too the two batteries in parrallel. So the radio never has any draw on the starting battery.

If the bat switch is setting on BOTH then the alternator connection is tieing all batteries together. If the bat switch is in 1 or 2 then the alternator is charging 1 or 2 depending on which bank it is switched to. So long as you're switching the bat switch to the start battery bank when you stop, you should be fine when ready to head back in.

I run 2 house batteries, and 1 engine battery. I turn the Perko switch to house while sitting and put it on both when I fire it up to leave. I put it on both because they say never switch the Perko switch while running.