First and foremost, go Wings! Isee you from Buffalo, I live in Rochester.
You don't necessarily "do" the abilities. The abilities are basically just your number rating like in Madden. APF did away with the numbers and abilities determine how good a player is. If a player has deep threat and speed burner, he's gonna be a really fast guy who can catch it downfield. If your QB has a laser arm, he'll be more accurate with not much power.
There's also abilities that YOU activate. Like signal stealer (press X before the play on O or D) or one of the defensive line moves (like swim, club, which are activated by charging up and pushing one of those buttons).
For further questions, go to the "how to gameplay" thread.