Your understanding is correct regarding the phase change. But changing just the output to negative will not serve the purpose.
PID source code might not be developed to take care of negative number.
If you are looking to change the speed based on the potentiometer, lets say you need to be at zero speed at potentiometer mid point and opposite speed at both end.
You can try changing the void Adc_MotorCurrentSense(void) function.
Here Motor_u8RunningDirection is used to vary the motor direction. You might be able to use the potentiometer position itself for determining the direction. (if the potentiometer value is less than half --> direction = CW, else direction = CCW)
This is just a vague idea and might needs to take care of many potential issues. Hope this helps.