Normally, you should not seal the bottom of the rub rail. The rub rail is the seam where the top part of the hull is attached to the bottom of the hull. You do not want to trap water behind the rub rail as it may get into the fiberglass. On most boats, the top of the rub rail is sealed with a thiokol-based polysulfide sealant like Boat Life, never silicone. This stops water from getting into the seam. The bottom is left open so that if water does get in, it has a way of getting out.