First remove the manifolds from the engine. Plug the one water inlet. Now take about 5-10 psi of air and blow it in the other water inlet. If you can hear air coming from inside the manifold it is cracked inside. It either has frozen or got real hot then was hit with cold water.
The flappers go on the back of the boat on the outside of the exhaust tips. This keeps water from coming in when backing up.
What motor do you have?