Expose the stringer. This may mean you have to cut out a piece of decking with a reciprocating saw or rip out interior panelling to expose the area. Expose all areas of the stringer where rot is apparent even if it means uncovering the whole length of the stringer.
Cut away any fibreglass that wraps around the stringer with hacksaw, coping saw or a small battery powered saw. The stringers can be wrapped in fibreglass before the fibreglass of the boat hull or deck is laid down.
Inspect the wood stringer for damage and locate the rotted areas. Drill holes in the top of the stringer in the rotted areas with a drill. Drill holes every 15 to 25mm apart through fibreglass. The holes should be 5 to 10 mm in diameter. Sharpen a point on a old screwdriver and brush it into the holes. If the timber is rotten the sharpened tool will easily penetrate. Allow the holes to dry completely--use a hair dryer to expedite the process. My preferred technique is to place plastic over the holes and seal it on then hook up a vacuum cleaner as the vacuum will draw all of the moisture out. Whereas the dryer will take ages to release the moisture to dry out the stringer.
Fill a large syringe with Bote Cote Marine Epoxy with TPRDA added and inject the Bote Cote into the holes. This will take several applications as the rotten timber will soak up heaps and it takes time for the timber / rot to become saturated. Allow the Bote Cote to cure for at least four days.
Use a paintbrush to seal the exposed areas of the stringer, including the holes, with Bote Cote epoxy.