For many of the films I've worked on I've produced what I call "hybrid scores" - which are musical scores that combine both live orchestral recordings and synthesized elements. Scores are prepared to an almost complete state using MIDI sample libraries and then certain layers are replaced (or doubled) with live players to give it that final touch. Samples are great, but there's nothing like real musicians!
During the recording sessions, it's important for each moment of the music to line up correctly with the film (obviously). Each cue is prepared for the recording session by creating click tracks for the musicians to play along with - including countoff clicks and any tempo changes. Also, many times the film is projected above the musicians to help the conductor to control the special nuances of the music.