How do we know which terrorist flew the airplane into the 2nd WTC building if no witnesses survived?

It is reported by the FBI that Marwan Yousef al-Shehh was flying the plane that crashed into the 2nd world trade center building, the one at the perfect angle, which caused it to collapse before the first building that was hit. Marwan Yousef al-Shehh was 23 years old and had only studied flying on a flight stimulator the last few months of 2000 and had moved to the US in 2000. How could someone that young and inexperienced fly a commercial 747 without GPS, completely manually and hit the target at such a fast speed while flying over an area he had never flown before? And how is it the FBI is certain enough to state he was the pilot and how did Mohammed Atta's pport survive the flames from that airplane crash, as it was discovered on the street below the tower amid all the dust and rubble?