Been in the cockpit of an AA B767 on the same type of clear mornings more than once. From where they took over, you can see straight down the Hudson river to Manhattan. The streets also gave a perfect aimpoint for flight 11.
The Pentagon plane was a little different. They obviously knew the basic FMS steps to go direct to DCA. There was some talk that the circle maneuver there was due to them being unable to find the White House. It is tough to see the first time from the air. The Pentagon is easy to pick out though.
My bet is they had a decent FMS program simulator, or had some late night access to a middle east carrier's 767 or sims from a sympathetic employee. It would'nt take much to learn the basic steps to point a Boeing the right way despite what the loose change idiots think.