I'm no expert at ffmpeg, but Matterhorn distribution media files do not have matadata attached to them. It would be great if this could be done based on the mediapackage metadata, then when sharing the file(s) people can use their media players to get details on recordings. Eg. when user imports the file into iTunes it automatically added title, album, etc...
Use the -metdata "title=SOME_TITLE" switch for ffmpeg
See eg documentation at: http://rob.opendot.cl/index.php/useful-stuff/ipod-video-guide/
For one pass:
ffmpeg -i INPUT -acodec libfaac -ab 128k -s WIDTHxHEIGHT -vcodec libx264 -vpre slow -vpre ipod320 -b BIT_RATE -metdata "title=SOME_TITLE" -threads 0 -f ipod OUTPUT.mp4