I'm not sure what you're talking about here. The factory exhaust is below water level until you get it up on plane. So are you looking to get the exhaust below water all the time or are you just wanting to make it quieter after it's on plane?
To put the exhaust below water level all the time would require something like a FAE exhaust system like this:
http://www.freshairexhaust.com/The problem is that they aren't cheap and you have that God awful pipe hanging into the water all the time.
The other option is to just put quieter mufflers on the exhaust. the factory mufflers are quieter than straight pipes but not a whole lot. You can get aftermarket mufflers that would quiet it down quite a bit. It all depends on how much you want to spend.
I just don't understand why people want to do this. That's the biggest draw about these classic boats to me. The sound. Nothing sounds as good as they do. Hot rods on the water.