The best stuff I have found to fix gaps, cracks and holes is epoxy putty.  I comes in a roll and you have to kneed it to activate it.  After its been activated, you have about 15 minutes to work with it on what you are repairing.  It cures in about 20 minutes and is good to go in less than 24 hours.  It is completely sandable and can be used below the waterline, in or out of the water.  It is super easy to work with and you don't need to worry about any nasty vapors.