I'm into car audio & I also live off the grid on a solar system, so I deal with draining batts on a daily basis.
I can basically tell you this, if you get quality deep cycle batts and keep them charged (like everynight) you should be fine.
I have four, 6 volt, 400 amp hour deep cycle batts that run my whole house. They are wired two 24 volts. I run a 37 inch flatscreen, luxury gas oven, lights, full size electric refrigerator, etc.
I also have a Honda EU3000 generator hooked up to an Outback pure sinewave inverter/charger.
I run my generator 3 hours a day when I get home from work and that lasts me till the next day after work.
What I'm trying to say is if you drain your batterys and then charge them in a timely manor, you'll be fine. If you discharge then wait too long to top them off, that's when you cause damage.
About the alternator, if your ever at any time using a stock alt to charge a very large DEAD battery bank, you will kill it and find yourself buying an HO very soon.