Yep, you'll be able to use them perfectly. Rudder pedals are almost mandatory for playing the game on expert (the hardest difficulty) because of the torque induced yaw modelled in the game, plus it should make aiming at things easier (if you end up using combat helicopters).
Just make sure that if you find flying too hard at first, that you set the difficulty down a bit, since that makes the flight model a little easier. Also, you might want to adjust the deadzone of your joystick to be zero (i.e. no deadzone), if possible - I find it makes hovering easier and certainly is more realistic.