And the answer to the question is found only in the Letters. I don't have the Letters, perhaps Jen or Overtaxed will post it?
For the record, the answer suprised the heck out of me. I thought wrong all these years... As does Jackson in the film, and many other fans... I would have thought The Two Towers were Orthanc and Barad-dûr .
"The second part is called The Two Towers since the events recounted in it are dominated by Orthanc, the citadel of Saruman, and the fortress of Minas Morgul, that guards the secret entrance to Mordor...."
Did Tolkien write that note, or did some nameless editor?