I tried to google the phrase "everything is everything" but can't find its origin. Where does this phrase originally come from? What does it mean?
Google books search shows that "A Disciple", in an article entitled "Emerson's Essays" which appeared in the June 1845 issue of United States magazine and Democratic review, wrote
... as a recent critic on the "Teutonic Metaphysics or American Transcendentalism" has satirically expressed it, "everything is everything, and everything else is everything, and everything is everything else."
I have no idea who this critic was. The expression is simple enough that it might have been coined independently several times, but if this was the original coinage, it cannot have been earlier than American Transcendentalism itself, which puts it 1836 or later.
Note that it's easy for an expression like this to change from a negative to a positive meaning. For instance, "the Big Bang" and "abstract nonsense" were originally expressions meant to slight the Big Bang theory and certain types of argument in mathematics, respectively, but which are now used positively by people in their respective fields.
According to Urban Dictionary, this is a hipper version of "it is what it is" or "que sera sera." If that is accurate, it could be either a resigned statement of the inevitable state of things, or a content acceptance of reality.
First I ever heard it was the 1989 movie An Innocent Man, where one convict is getting the crap kicked out of him and the bad guy tells Tom Selleck that if he causes any trouble, he's next, but if he cooperates, "Everything'll be everything."
It seems to mean "Don't worry, nothing will happen."
In the context of An Innocent Man (answer by @Malvolio) for instance, the bad guy is assuring Tom Selleck that everything will stay as it is (nothing will happen to anything) if he co-operates.
By implication, he's warning that he better co-operate or things could get unpleasant, like what he's seeing now.