what ridge said, but i did mine from the top. i have a cuddy, but the methods the same. cut out the bad area until you get to good wood. epoxy some cleats or a lip around the bottom of the existing wood in the hole. cut a new piece of ply to fit the hole. wet it out good and place in hole. wet out pieces of cloth and build up to current deck level, then fair with putty. the main drawback is you then have to paint the deck and once you paint, you will always have to repaint later. if you re-coat with the kiwi or durabak or similar product, would most be likely a one time deal.
since you have a center console, you don't have much room to work with between the console and the gunnel so removing the console would probably help a lot. if they just screwed the console to the deck, that's most likely where the water intrusion began.