As with anything in this game, a change takes a long time to become second nature. As the others have said, it'll get better after the initial unfamiliarity, and once you get used to them, there are a lot of things that are easier to do than with a twisty, like keep a constant rudder through a maneuver independent of your stick inputs.
I had been flying with pedals for around a year and a half, and had to use a twisty at one point away from home. It amused me greatly because every time I'd go to bank the plane, I'd kick the floor expecting a rudder pedal to be there.
Wiley.