When PJ was a teenager, he was abused/raped.  This trauma created as teenager a self-defense personnalty: Red John, the bad PJ took over and put somewhere in the head the original PJ like a puppet.

Because guilty, culpability and the trauma with the kill of wife and child of PJ (which was the public RJ cover) it was to much for a young boy to manage with, the puppet/original PJ manage to create the nice PJ as we knew in the show as attempt to stop the bad PJ/RJ.