You guys that think that red john is an alternate personality to patrick jane , you are forgetting that redjohn killed people BEFORE killing patricks family , and also , the only reason he did it was because patrick talked about him on tv , and about being an effect of his breakdown , his breakdown was BECAUSE of the killing of his family by Red John
my true theory tough is a whole net where there are 2 arms of red john , where 1 is vizualize and all under it , while the other is the fbi and cbi agents 
on the vizualize side Stiles knows RJ , rafner is a pure follower of stiles , doest not know red john
on the fbi/cbi side bob kirkland is submitted to some woman that knows red john (as we see in a flashback in a limo) and under bob comes the little 3 way network that we see in the 6x02 ( bertram reed and mcalister)
PLEASE POINT FLAWS