PID Controller

I have been working on a PID controller with an Atmel AVR Atmega8 microcontroller and 1.53:1 Gearbox Motor for several weeks now. The goal is to implement a PID controller in C code using the AVR microcontroller. The motor provides a quadrature encoder scheme for feedback. The AVR is setup with a Phase and Frequency PWM signal with a 2kHz period for motor speed control. The Duty Cycle for this signal is controlled by a trimpot which is sampled by the on-board A/D Converter. The direction of the motor is controlled by a Port Pin in code.