Your alternator is working.....
You bought a boat with a short in it. This is why people sell boats.
not to worry, we can track it down. Your gauges freaking is the intermit short, shorting out, other wise you every thing is fine.
First:
1. never run on both batteries.
2. disconnect all wire off the battery, let it sit over night, to make sure the batteries are good the next day.
3. connect one wire back at a time, one day at a time at the dock. You will enerigize each curcuit one, by one, until the problem happens again.
4. after you try it on all those wires hanging off the battery post, then then next step is to pull all the fuses under the dash, and then install them back one by one, to enerigize each curcuit.
It's not the engine harness, since the engine did not die.
It could be as simple as a shorted horn, or the carbonmoxided decetor past its 5 year life.
wigggle all wires you can get your hands on and look for burned or hot to the touch.
stick your head under the engine and look at your starter, this 80amp fuseilble link is the thing that holds all the amps back from frying your harness. if it looks burned or melted, then that your problem.