[deltacoder1020]

well, the PID control loop code you saw on the NRG repository essentially accepts a requested (nominal) PWM value, and the actual PWM value (in your case, from the encoder) - the second two variables are just for storage (note, you could just declare these in the function as static variables instead of declaring them elsewhere and passing them as arguments). It then returns the value that the PWM should be set to. It's essentially that simple - call it with those two values, and set the pwm variable to the return value of the function.