Barad-dûr: one tower. Orthanc: one tower. Barad-dûr + Orthanc: two towers. Okay, we're glad we cleared that up; math can get pretty confusing when you're dealing with small quantities of massive towers.
But honestly, there's really not a whole lot more to it than that. Tolkien's second book was focused mainly on the threat of Saruman, who operated his army from his fortress Orthanc in Isengard. In The Fellowship Elrond doesn't believe Rivendell can defend armies from both Isengard and Mordor; it's Saruman's betrayal that ultimately forces the Ring to be carried toward Mount Doom in a last effort to win the war before the free people are overwhelmed.
We don't see as much of the second tower, Barad-dûr, during the film. But with Isengard being flooded by the ents and Mordor's armies on the move, we get a feeling we'll be seeing more of everyone's favorite giant red eye in the final film.