for an amplifier, you take wattage/ amp efficiency, (80% is a fair number to use, but you can usually find yours to be accurate). Then divide that by voltage = amperage draw.
If it's a 1,000w amp,
1000/.8 = 1250.
1250w / 14.4v = 86.8 amps. (the slightly overage estimate is 9 or 10 amps for every 100watts).
Your stock alternator is sized so that if you have everything going you have enough. Your EFI, lights, AC, horn, turns, cig lighter you are probably around 80amps.
If you have a 1,000w sub amp, it's only full draw on heavy bass notes. Between those bass notes it's using less than your alternator is charging. If you listen to heavy bass music like rap, it's going to draw more often. There's a few factors that you need to consider. Maybe it's a winter beater and you don't use AC. Maybe you buy a really efficient amp, or a really cheap one. My guess is somewhere between a 500-800w total setup would work with that alt, and not cause problems.
A second battery is just a storage bank. If you put in a 2K watt system, with that alt, you're just going to kill two batteries, it will just take a little longer.
Not sure what your plan was, but I think that alt would work with a system that's a single 500w amp, with a 500w sub, and something around 80-100w per ch on a second amp for door speakers, maybe a 4ch amp.