National Security Advisor and, it seems, Mr. Zelikow was working for her in re-drafting "an overview of America's national security strategy":
In Rise of the Vulcans (Viking, 2004), James Mann reports that when Richard Haass, a senior aide to Secretary of State Colin Powell and the director of policy planning at the State Department, drafted for the administration an overview of America’s national security strategy following the September 11, 2001 attacks, Dr. Rice, the national security advisor, "ordered that the document be completely rewritten. She thought the Bush administration needed something bolder, something that would represent a more dramatic break with the ideas of the past. Rice turned the writing over to her old colleague, University of Virginia Professor Philip Zelikow." This document, issued on September 17, 2002, is generally recognized as a significant document in the War on Terrorism.
http://en.wikipedia.org/wiki/Philip_ZelikowFrom the Washington Post article yesterday:
Condoleezza Rice, John D. Ashcroft and other top Bush administration officials approved as early as the summer of 2002 the CIA's use at secret prisons of harsh interrogation methods, including waterboarding, a technique that new Attorney General Eric H. Holder Jr. has described as illegal torture, according to a chronology prepared by the Senate intelligence committee and declassified by Holder.
http://www.washingtonpost.com/wp-dyn/content/article/2009/04/22/AR2009042203141.html?hpid=topnewsLooking at the dates when Mr. Zelikow was doing the re-write and when Ms. Rice approved the torture, Mr. Zelikow would have been working for Ms. Rice at the time she okayed it.