if you would like to see how ffmpeg works for you, you could use the syntax:
Code:
ffmpeg -i handbrakefile.mp4 -i commentaryfile.mp4 -map 1,0 -c copy newfile.mp4
'-i' quite obviously specifies the two input files, '-map 1,0' specifies that the 2nd input file (commentary) be synched to the 1st input file and '-c copy' specifies that no re-encoding be done. Therefore this command line assumes your commentary track is already in a format suitable for MP4 and iPad.