But that's actually beside the point now. You've started this story with some serious wham's, Clark's parents potentially dead, Lois married Lex Luthor, Lex Luthor president. Or former president? I don't know the proper way to address the president's wife but is it really "madame president"?
It seems pretty obvious to me that
Lois is the President, not Lex.
"Madam President" (no 'e' at the end) would be the correct way to address a female President. The First Lady or First Gentleman is addressed with his or her name, e.g. "Mrs. Bush."
In regard to this, I have one minor quibble (if Lois is indeed the President): an assistant would in all likelihood not use the President's name when speaking to him or her, only "Mr. President" or "Madam President" (or, alternatively, "sir" and "ma'am", respectively). I realize you wanted to build in the information about her being Mrs. Luthor, but I thought I'd let you know.