Ok, Well I'm guessing your not familar with Lex's cloning storyarc from the comics and that's why this is confussing to you .
Well I hope my explanation helps.
In the 1990's revamp of the Superman comics
Lex Luthor acquires the only known sample of Green Kryptonite on Earth at the time from the Kryptonite-powered cyborg Metallo, whom LexCorp abducted just before Metallo almost succeeded in killing Superman. Lex pulls the Kryptonite out of Corben's chest violently remarking if anyone was going to kill Superman it would be him no one else .
Lex then Fashions a ring from the alien ore deadly to Superman, Luthor began wearing it constantly to ward off his enemy.
Unfortunately, Luthor began to suffered from a severe cancer in the 1990s, caused by long-term radiation exposure from his kryptonite ring. (Before Man of Steel, kryptonite exposure had not been thought to be harmful to non-Kryptonian life forms). Luthor's hand had to be amputated to prevent the cancer's spread, but unfortunately by then it had already metastasized; it was eventually determined that the disease was terminal.
Lex Luthor faked his own death shortly afterward by taking his personally designed jet, the Lexwing, on a proposed trip around the world and crashing it in some mountains, using this as cover for the transplant of his brain into a younger healthy clone body of himself which he then masqueraded as the illegitimate Australian son and heir, known as "Alexander Luthor" his new body appearence of having a full head of red hair and a beard helped sell his deception to the public (with the exception of Lois Lane, Superman and Batman who weren't conviced by Luthor Jr.'s Charade .)
Lex Luthor used his new identity as his own son Alex to seduce Supergirl and continue to torment Superman from the shadows. However everything quickly fell apart, when Luthor's new clone body began to deteriorate and age at a rapid rate (his being one of many clones that were becoming ill at the time). This caused Luthor to begin to slip, as Lois Lane discovered proof that Lex Luthor had years earlier murdered a female LexCorp employee and framed an innocent man for the murder. This led Lois to find out the truth about Lex faking his death and being his own son, which caused Luthor to systematically destroy Lois' life and have her fired from the Daily Planet. Lois fought back and with help from Superman, exposed the truth about Lex Luthor, his faked death, and his evil criminal activities to the public.
Right before his body became so old that he couldn't move or communicate, Lex activated a "Doomsday Plan" to destroy Metropolis. The city was burned to the ground and thousands killed as Luthor became a permanent prisoner in his cloned body.
However, aid would come in the form of the demon Neron; Luthor promptly sold his soul in exchange for Neron restoring his body to perfect health. Returning to a rebuilt Metropolis, Luthor turned himself over to the police and was put on trial, where he was acquitted of all crimes when Lex Luthor claimed to have been kidnapped by renegade scientists who replaced him with a clone, who was responsible for all the crimes he was charged with Luthor was free to return back to business at LexCorp, However he decided too instead take up politics...
In Smallville, The Producers as well as Tom Welling realize the importance of Lex Luthor's character to the Superman mythology have decided to bring the character back regardless if Michael Rosenbaum decides to returns to the role or not . This Clone story arc is the producers way of stalling until they can either get Michael back or they recast for the series finale .
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