I think there's a million ways to use the deck.
The most common ways I've seen are shuffle when one of the extreme cards comes up (++++, 0000, ----) or when the deck is used up.
But there's all kinds of fun stuff you can do. For example let people hold 5 cards and let them spend a fate point to discard everything and redraw or draw additional cards, to increase your odds.
You could also introduce stunts that play off the cards, like allowing you to keep a card after playing it.
All in all, the deck can bring a whole new dimension to the game.