This idea is underscored even in the sets that it gives its two main locations: cool tones for Metropolis, warm tones for Smallville. In this way, the Manichean impulse toward the inevitable struggle between good and evil that rules all comic book descriptions of Superman and his Luthor is carried through, into a much more complicated medium. However, to fully realize the potential of this twinning motif, Smallville uses it over and over again.
The notion of dualism is, naturally, extended into the idea of split personas -- public masks, and private lives, which is (of course) the main theme of the mythos from which our show is formed. We have two characters (Clark and Lex) who we *know* will be living double lives in the future, but who *now* must contend with the dualistic sides of their personality.
Lex lives a double life as a public figure (mayor/president of lexcorp/president) and as an archnemesis to Superman. He maintains an (at times) dubious public persona, but the depth of his involvement in crime is kept secret -- if it wasn't then how the hell could he become president? Clark's double life is a rather obvious one -- that of Superman and Clark Kent, of course.
So you have these two figures who separate their Godheads from themselves -- Superman and Luthor, vs. Clark and Lex. Their violence and primacy is separate from their mundane existences. So they are primarily dualistic personalities. Now, going with that -- Smallville is attempting to establish a parallel wherein they are the Cain and Abel paradigm. Which is another form of dualism, but I won't go directly into that, yet. With these two boys we have a variety of instances wherein they are splintered, twinned, and doubled.
Additionally we are given several characters who act as good twin/bad twin -- you have Jonathan Kent and Lionel Luthor, who certainly share a bond and could be seen as two aspects of the same figure; good father and bad father. And then there's Chloe and Lana -- who AlMiles have said combine to create Lois Lane, so basically they've acknowledged that these two girls are two faces of the same person, much like the above.
Now what does all of this mean on a weekly level? How does Smallville work it into the story lines of it's episodes? Well, first it parallels the two boys -- giving them a single Janus-faced father, if you decide to amalgamate Lionel and Jonathan into the overall archetype of Father; wise, powerful, loving and terrifying. *And* it puts them (Clark and Lex) into similar situations, showing again and again their similarities -- but further than that, it gives both of them alter egos at the start of Season 3. Clark has Kal, and Lex has Louis.
With both of these half-selves that the boys have they have forcibly separated from themselves the negative aspects of their personality. What is significant for the way that their lives will progress is how they choose to deal with these phantom selves.
Lex confronts his phantom self in a physical battle -- he attempts to tangibly destroy it, and in doing so, he refuses to acknowledge it. He doesn't re-integrate it, he remains incomplete, and refusing to deal with all of the implications of this splintered self. And in this way, he is left vulnerable, as he is never complete -- there is an argument to be made here that this is why it is, then, that this negative side of him ends up gaining the upper hand in his psyche.
If we were to treat this as myth, then we could say that Lex's attempt to kill Louis as a repudiation, and that by repudiating Louis he turned Louis into a whole other being -- a seperate self, who then combats Lex all over again, slowly grappling with him as a shade or ghost that haunts him, and eventually triumphs at the close of the series.
As Season 3 progressed, Lex was broken down further and further -- already not a complete whole, he was 'shattered' by the events of the season. If one were to read even more mythology into it, it could be said that his vulnerability (created by the exorcism of his literal demon) is what lead to the invasion of insanity. It's as though Louis -- his negativity -- stood as gatekeeper to his soul, and in his stead there came a steady flood of other demons, all at the behest of the Terrible Father Figure.
On the other hand, we have Clark, who does not go into physical battle with Kal, his phantom double. Clark, instead, chooses to incorporate Kal into his full persona -- in fact, at the end of Pheonix he verbally acknowledges that Kal is part of who he is. In his behavior throughout S3, we see Kal peeking out time and again. This makes Clark stronger, a complete and *whole* person, and therefore not as vulnerable as Lex to the whisperings of his shadow self.
I see Superman as Clark's Godhead. Superman is the divine within Clark -- the sublime that cannot be recognized within his aspect of mundanity (the reporter guise). He is the every-man and the godlike all at once, so I would say that Superman is part of Clark's singularly dualistic persona.
Ultimately, though Lex and Clark are two divided personalities, they are also two parts of the same whole. Even if you don't ascribe to the fanon romantic relationship, they are certainly two of a kind -- sons with destinies, and as we see them move toward their futures we also see them become one another's doubles, and phantom selves. Clark is Lex's conscience, as his own atrophies and falls away, and Lex is Clark's muderous impulse. It is Lex who keeps Clark honest -- as Lex posits during Talisman -- and Clark who will keep Lex from taking responsibility for his actions.
All of this discussion of Clark and Lex as one another's phantom doubles, or shadow selves, serves only to underscore that their desire for one another -- desire to kill, or fuck -- comes from a place much deeper than betrayal, or hurt. It comes from a primal desire to merge (as Clark did with Kal) or destroy (Lex and Louis), and the reason that ultimately neither of them can prevail is that for the both of them to go on as a balanced pair (an equatable equation, really) is for them to remain s they are; as matched set, two faces of the same divinity -- the god of Metropolis, both kind and cruel, fickle and perseverant, wholesome and jaded.
It means that those who serve Lex serve Clark, also -- as do those who work with Clark and Superman. It means that Mercy Graves is a priestess of Clex and so is Lois Lane. Clex, like Kali Durga in India, is the god of love and war. A god who creates, and who destroys, and what is interesting about it is that Lex is the creative aspect of their whole, while Clark is the destructive one.
They are an inversion of one another, and in all honesty, at the core, they carry out one another's deepest held fantasies. Who they are to one another -- their opposition -- is what creates the men we know, the men we find so endlessly interesting, and nothing else. And this is why -- this ever so fragile balance that exists between the two -- they *can't* just forget the past, and move on to the future. If they did that, they would almost cease to exist.
But, even if Clark and Lex could go on from a merging, their divinity would disappear. They would become only their mundane selves, without the powerful godliness that defines them.
To become the domestic lovers that so many slash fans would want, they would have to be *only* that. They would have to forsake, for lack of a better word, their greatness. An easy analogy to make would be that of Achilles, told that if he goes off to war his name will be remembered for centuries to come, but if he stays home he will be loved. He chooses to go to war, just as Clark and Lex do. War is the way they love each other, in the end -- through their violence to one another they provoke that which is sublime in the other. Each blow is a caress, each bullet is a kiss, each plot is an elaborate way of saying 'I love you', if viewed in this context. Their tenderness is transmuted into violence, and so one must view their violence as tender.