In our shop, when we get a deep scratch, we first make sure that the area is dry. If the scratch is deep, and has exposed fiberglass of even to wood, dry the area for a couple days. Once dry, sand the area to remove the varnish. Sand an area larger than the area you intend to apply epoxy. Apply epoxy to the scratch generously.
Once cured, you boat is ready for the water again if is the middle of your paddling season. If not, lightly sand the area and apply a couple coats of varnish.
Dave @ Pygmy