Mask off each side of the deck as close the seam as you can get...then putty. You might want to put a backing piece of plastic, a scab, to prevent seepage. I don't remember if the deck has those molded in or not.
Once that's done, fill carefully and wet sand. When it's done, remove the tape. You may have to replace the tape a few times to protect the surrounding deck area.
Jeff Herne