You can seal both sides if you like but it's not nessesary. If your using CA hinges, the CA glue once applied during installation will harden the hinge so if any residue from the exhaust gets to the hinge it will do no damage. If it does then the hinges were not properly installed. Been doing this for over 15 years, never has a problem with sealing the bottom only. All it's for is to keep the air from passing through and causing flutter. It also makes for a more stable flying plane.