The output of the phase comparator is high when the 2 phases being compared are different creating a duty cycle that is equal to the difference. This can then go through a low pass filter to average it out to a DC voltage level representation of the phase difference that can be read by a micro controller's ADC or a VCO to make a PLL.
If you have 2 sine waves I find it best to use a voltage comparator to convert them to square wave pulses before going into the phase comparator.
Turn up the delay % of the green pulse to increase the phase difference, increasing the duty cycle of blue and the voltage of red.
