Sounds like you have a wood core covered by fiberglass. If the rest of the hull seems solid, you could replace the core. The strength usually come from the wood core. Often it is fiberglass underneath, plywood, and another fiberglass layer on top to seal the wood from water. Think of your deck as a wood sandwich, in wich, the bread is the fiberglass.
It is possible to cut out the top layer of fiberglass, replace the wood, and re-seal the wood with fiberglass again. it depends on your fiberglassing skills and how perfect you want it to look. My guess would be that water got into the wood around the screws that bolt the helm seat to the deck. Take a rubber hammer and tap a known solid section. Know, tap the known rotten section. Copare the sounds. Now start at the soft section and tap until you find that solid sound. This will be the area that needs to be replaced. Try to determine if it, in fact, is wood between 2 layers of glass. You can do a drop cut with a circle saw to cut loose the top layer of glass only! You should only be cutting about 1/4" deep.Peel up the top layer of fiberglass with a wide wood chisel and hammer. You want to save that top layer, if it has a "non-skid" pattern molded into it. Dig out all of the rotten wood. This could be plywood or "balsa wood core" material. Dig out all of the rotten wood, so that it is even with your top layer removal. Let the new hole area dry out in direct sun for several days. You may use heat lamps to speed the drying time. Once you feel that the area is good and dry. sand the exposed bottom layer of fiberglass ( back side of your fiberglass/wood sandwich) with 60 grit sandpapaer to scratch it up. It gives the new fiberglass something to stick to. Acetone can be poured around the edges to help dry surounding wood edges and clean the entire area (careful-very flammable). Now, replace the missing wood. Get plywood or balsa core that is the same thickness as what you took out. Cut it to fit as perfectly as you can. I would use "west system epoxy" for resin. Mix a batch up with micro-fiber filler or silica additives. (The west system web site explains all of this) to a thin peanut butter consistency. Cover the exposed bottom layer of fiberglass and edges with this mixture about 1/8" thick. Push you newly cut wood replacement into the cut out hole and sit something heavy on it. The mixture of resin will squish out a little. Use a putty knife or plastic spatula to remove any excess above finished deck level. Fill all gaps between the new wood and old wood with this mixture. Scrape off any extra rsin from the top of the new wood and let it cure for a day. I would then clean and sand the underside of the removed top layer of the old fiberglass deck. Make another batch of the thickened resin and cover the new wood maybe a 1/16th. inch thick. Set your old top layer of fiberglass deck into it's old place and weigh it down with sand bags or something to hol it in place. Let it dry. The objective is to get the patched area exactly level with the sorrounding deck. When it is all dried. Sand about and inch or 2 on both sides of the cut out patch. Take about 1/16th. inch of fiberglass away from each side of the patched area. You want to remove just enough material on both sides of the lines that you initially cut with the circle saw, so that you can cover it with a layer of 6oz. fiberglass cloth/with resin." Kind of like, taping a joint in drywall work". You should be able to sand and fill any remaining imperfections until very smooth again. I would paint the area with "Interlux perfection" 2-part epoxy paint. Pick a shade of white (assuming it is white) that is close to the gell coat color as possible. Try to paint an area around the patch that will blend in best with what you have. You may decide to paint the whole deck.
That is the basics of what is involved. There are many videos on "you-tube" that show how this is done.
Good Luck!