I think if you can retreive your boat quickly, leave it open. Fresh air is great, but only if you have a boat to jump in and grab it. A new motor is always cheaper than it's vehicle. If your running big water, tape or cork the tubes. No point in sinking FOR A MOTOR!
BTW- I have tried a bunch of different kinds of tapes. Strange as it is that hockey tape is awesome! This link will get you to a company that sells the hockey tape in a big roll. I think it's five or six dollars, plus four for shipping. I promise, It's worth it.

[link]http://Offshoreelectrics.com[/link]