Hi blunas;
Well if water came out my bet is there is more water in their then you might think.
If I were going to do just a patch job I would cut the top lamination (skin off the deck). Not knowing your boat, for me, I would cut at least twice the size you think you have a problem out. So if you have a 1’ square soft spot cut 2 square foot out of that top lamination. Then use a chisel and remove the balsa wood or ply wood you have in there until you have no soft water spot. Then get some ½” marine grade plywood and coat both sides with epoxy or you can get some composite material for decks. Then with thickened epoxy put it in the hole and then thickened epoxy to put the old deck skin in place.
Go here
http://www.westsystem.com/ss/use-guides/
and read this
002-550 Fiberglass Boat Repair & Maintenance
FellowShip
Just for the Grins