I assume you mean you have a wet wooden core in the deck?
You have to cut off a section of the outer fiberglass skin lather than the soft spot, either from above or below, replace the core and patch the skin back on. From above, it's easier to make the patch, as gravity is on your side. However, being exposed, the patch can be very hard to make undetectable, especially the gelcoat. Impossible, if you have to patch in molded non-skid. From below, you may have a headliner that disguises a less than perfect patch, but working upside down is tough.
Some will recommend trying to bond the old skin back on after replacing the core, but that rarely works. There may be spots in the middle of your repair area where the core is still good and bonded, and this will make it nearly impossible to get the skin off without breaking it. Then after the repair it's very hard to get the skin bonded back on properly. You also need to taper back the edges of the remaining skin to allow the new repair to bond in, which negates most of the advantage of reusing the old skin. Better to plan on laminating on a new skin from the beginning. Slightly more material cost but much easier.
Some will advise to drill holes and inject epoxy mix, but don't do this. It rarely works, and is a kludge that will make a proper repair much harder! How big is the area? What kind of boat? There are different things you can use as a core, Balsa and Plywood are most common. Some here have had good luck with a honeycomb material, search for posts by Caleb, he did his decks and seemed to get the work done quickly, or so it looked via the internet!
Working with the polypropylene honeycomb core was awesome. It cut easily with a sharp razor. I found this stuff at an outfit in Michigan: Express Composites which another boater introduced me to.
I couldn't agree more with capt jgwinks about NOT re-using the outer skin. The side I did without using the old skins is done. The side I did re-using the outer skin needs to be re-done around the seams.