Answer:
The first tower is Barad-dur, the great fortress in Mordor where Sauron dwelt. When, in the movies, we see the "Eye of Sauron", the tower it is on is Barad-dur.
The other tower referred to is Orthanc, in Isengard, where Saruman the White lived.
The second book takes its title from these, since Sauron and Saruman are the bad guys. It must be noted that Saruman is much, much less powerful than Sauron, and is defeated by the end of the second book.
The two towers that are most important in the book the two towers are Orthanc and the Hornberg. Orthanc is were Saruman dwelt. The Hornberg is the tower in Helms deep.