@RickLip: Mayhaps, but whereas Demon Seed just shares the same topic, the references in Underneath It All are outright blatant: "Numb all through / I can still feel you"; "Kill my brain / Yet you still remain" - compare these with I Do Not Want This and The Downward Spiral (the titular track), respectively.
@DoubleGJ: I guess you're right. Demon Seed also is about some indifference growing inside of the narrator. (Just compare them both: "All I do I can still feel you" vs. "It keeps growing I can feel it breathe")
In my belief, this song is about how the narrator notices the indifferent part of him, even though he believed to kill it in the climax of The Downward Spiral, still is somewhere there in him - after all, this album is supposed to be a continuation to TDS, no?