To stack the deck could also mean to arrange things in your favor which is the most common meaning of the term. If you are a card dealer and you arrange the cards in the deck in such a way that you always deal yourself a winning hand, then you have "stacked the deck."

It means to arrange a situation in your favor or have it arranged against you. The expression comes from card-playing, and it implies cheating or unfair competition. If I say the deck is stacked against you, it means the odds are not in your favor.