Yeah, this is entirely a case by case basis. William & Mary said that if you submit electronically, then you don't need to do anything, as your electronic app will match up with a list they have of waivers, and you don't have to pay. If you send the app through the mail, however, you need to print the waiver email out.
So check with each waiver you have, and if it's not a clear answer, I'd call the school adn find out.