Peep sights are meant to be used as the rear sight. So, peep and front sight, dose, not mean you have to but regulating 3 sights is not going to be easy.

Looking through the peep you will notice a bright dot of light in the center of the peep; the top of the front sight should be in the middle of the bright dot. Doing this makes focusing on the front sight easier than trying to align standard rear sight and front sight, so the theory goes. This worked well for me when my eyes were a little younger. The bigger peeps were made for close, fast shooting, the smaller peep is for accurate distance shooting.