Adam, they will automatically charge your S&S when you arrive, but you can go to the Purser's desk and have it removed and tip them yourself the last night. I think in part it was instituted because people get so confused about tipping, and in part because some prefer to just stiff everyone. If you'd rather tip in person, that's fine too.
I chose to leave mine on and gave our waiter a little extra the last night. I'll probably do that with future cruises too, unless someone is just horrid.