If you want to use PID and you say you then want to change flap position every 60 seconds, what you need to do is firstly, operated the PID loop controller at a set rate, maybe use a timer interrupt, but importantly, you will then need to provide a new setpoint into the PID for the new position every 60 odd seconds for it to alter the flap.
Are you sure you need PID to do what you want, you know what PID is about?
Paul