i'm thinking a few pictures might help? there might not be a bunch about sail power i know of but i've been rebuilding cars since i was a preteen - smoking alts might be a rectifier problem or a voltage limiter problem. Even if the battery was backwards the diodes should have stood off the power unless they were bad. Granted you do horrible things to the battery doing that
There's usually a window on the alternator, i find near the back, that lets you look down inside the rectifier if its internal. older might have an external unit that has to be hooked up. anyways, in there you can see the pins that lets you get a volt meter on it and do a diode test.
either way you can get the alternator off the boat and to a local auto parts place - there's not many that don't have an automatic alternator test bed. You'll want it off either way to test/replace etc.
once the magic blue smoke is let free the genie no longer makes the mystery bits inside keep working. Given that i'm reading that the leading cause of boat loss is fire and that the leading cause of fires is electrical it might be time to replace anyway.