zipper: I thought the documentary said he did program the FMS to for direct to his target-- but he did have problems with aircraft control-- kept disconnecting the autopilot and then reconnecting after he had trouble.
The terrorist couldn't figure out how to shut the alarm off which went off every time they disconnected the auto-pilot....so they kept reconnecting the auto-control.
As far as the FMS (I don't know what that is), I do remember a pilot, I believe, saying that the terrorists had not figured out the GPS system (I thought that's what he said....is that related to the FMS? sorry, I am not knowledgeable of airplane equipment/technicalities). Their problem was not just with the autopilot alarm. And I do specifically remember the pilot saying that the terrorists were not used to flying commercial aircraft, and certain equipment that exists in commercial aircraft as opposed to smaller planes. If I understood the technical terms they used, I'd have remembered better, but that was my limited understanding.
EGPWS watched the documentary and is familiar with planes and equipment. I'm sure he wouldn't mind correcting my errors and explaining much better than I (though I believe he's offline for the evening).
I think you had that mostly right according to the way I remember them saying in the documentary. The autopilot disconnect warning kept going off and they couldn't figure out how to silence it (though it was only one button push). The terrorist flying the airplane wasn't used to that big of an airplane, especially at high speed, when it becomes much more pitch-sensitive-- and was having trouble controlling his altitude because of that. He was trying to descend the airplane, which meant the speed went up, which meant the controls became more sensitive. Then he'd put the autopilot on but that would level the airplane off, so he'd disconnect it again to descend, and so on...
But I think I remember the documentary saying they programmed the airplane for the target, or words to that effect. Once that is done there's a line on the navigation display that takes them on a track directly to the programmed waypoint.
FMS=Flight Management System and the navigational aids including the GPS are run through the FMS.
The FMS has a user interface control head to program flight itinerary for flight display, navigation, and auto flight control.
As far as the controls getting more sensitive at higher speeds, there is also flight aids that counter this also. When achieving a speed where sensitivity is an issue the flight controls in the cockpit (flight deck to those PC'ers) automatically stiffen up to prevent over control at such speeds.