Is this a delco unit? If so I found an old post by Oldsquirt when I was having a problem wiring my alternator(3 wire delco), I copied it to paste here:
"This is how I have always had my Delco alternator wired. Same setup, two different boats, 20 years. Look at the alternator from behind and with the connector facing straight up. The existing wire from ignition switch goes to the right hand terminal. You need to run a separate wire from the left hand terminal to the output terminal of the alternator."
After that run the output terminal to the + terminal on the battery.
As far as frying it. When I was toruble shooting mine I had it wrong a couple of times. I only ran it long enough to realize that it wasn't showing a charge though...