Whether this is correct or not I don't know but the origin of the phrase is suggested to be :

Got your six is a common phrase in police or military jargon, used to tell someone that one is looking out for their backs.

The phrase comes from the fact that airplane pilots used to refer to various directions around themselves as if they stood in the center of a clock; “in-front-of” became 12’o clock, while “behind” was turned into 6’o clock.