As an airline pilot, I can honestly say that I don't believe that the terrorists needed any experience of FMS programming, complex flight director or autopilot control or any other complex, airliner related systems.
Almost certainly, the aircraft would have been on autopilot when the hijack took place. It does not require the brains of an archbishop to steer it with the heading bug and then just hit the autopilot disconnect switch at the appropriate moment and hand fly it to oblivion. All they would need to know is a bit of basic straight and level, power attitude trim sort of stuff. Airliners generally need lots of trim changes with power and speed but again, anyone who has flown a piper archer or similar will, I am sure, be familiar with an electric trim switch.
I cannot believe that the terrorists would have even bothered with the FMS...what use would it be to them? It was morning on a nice clear day...I bet New York and the WTC stood out pretty well. Steer towards them, disconnect the autopilot and the rest is history! They would also have done their homework and known where they needed to head...even roughly would be good enough.
So it is all very nice wondering if they got information from PC flight sims. I personally doubt they would have bothered...a bit of basic flying experience and a look at a photo of a Boeing cockpit would probably given them all they would need to know. After all, we all know their intention...they were hardly going to set it up for a CATIIIB autoland were they?