Nine months after William J. Bennett took over the helm of the Education Department, several top positions remain unfilled because of resignations, congressional delays and the surprise decision of one highly-touted educator to say "thanks, but no thanks" to a high-ranking job.

Department officials said Senate confirmation of several nominees could get held up in the Capitol logjam until next year. Wendell L. Willkie II, Bennett's chief of staff and counselor, is awaiting confirmation as the department's general counsel. And Bruce Carnes, the budget wizard and acting deputy undersecretary for planning and budget, is still acting.

Meanwhile, Anne Graham, assistant secretary for legislation and public affairs, is awaiting Senate confirmation for a job at the Consumer Product Safety Commission.

Like complicated moves on a chessboard, those Senate-delayed confirmations have held up a number of other moves. Until Graham is confirmed, a long- rumored reorganization of her office has been put on hold. Until Willkie is confirmed, Bennett aide and friend William Kristol cannot move into that staff chief's job, as is rumored.

At the Office of Postsecondary Education, the assistant secretary's job is likely to remain vacant for some time. Bennett's choice, Spelman College President Donald M. Stewart, sent the department's personnel plans into a tailspin when he agreed to take the job and then unexpectedly backed out for "personal reasons." It was all but assumed that Stewart would take the job -- he even accompanied department officials on a recent trip to Japan for a major education conference -- but he decided early this month that he could not uproot his family.

Bennett met with Stewart but could not persuade him to change his mind. So while the search starts again, the assistant secretary's job continues to be filled on an acting basis by C. Ronald Kimberling, a former California Reagan-Bush campaign worker. Kimberling was not initially considered likely to get the post, since Bennett wanted an academic, especially a college president, to assuage the department's sometimes bitter relations with the higher education community.

Meanwhile, Harry M. Singleton announced that he is resigning as assistant secretary for civil rights after an often stormy 3 1/2 years defending the administration's positions on school desegregation cases. No successor has been picked.

Despite the shifts and delays, Bennett has managed to put his imprint on the department. His now-completed inner circle includes Chester E. Finn, the assistant secretary for research, and undersecretary Gary L. Bauer, Bennett's main spokesman on conservative themes like vouchers, school prayer and values in the school.

The Bennett team also includes a mix of old colleagues from Bennett's days in academia, along with trusted aides from his previous Reagan administration job as chairman of the National Endowment for the Humanities.

One newcomer who has broken into that inner circle and gained Bennett's confidence is Loye Miller, a former White House reporter for Newhouse News Service.

Miller, who usually accompanies Bennett on out-of-town trips, is credited with bringing a new kind of sophistication to Bennett's press operations -- avoiding the disasters of the secretary's first months, such as advising students to consider "stereo divestiture" to make up for student-aid cuts.

Miller is also credited with smoothing relations between the secretary's appointees on the fourth floor and the department public affairs office on the second floor. Whereas once the two floors were divided like east and west Beirut, there are now regular meetings, which Miller attends.