How do you handle picture-in-picture tracks?

[HStone32]

I have a couple movies in my collection that have come with an additional audio and video track intended to be played overtop the main feature as a visual commentary track (picture-in-picture). However, the method I used to obtain these videos did not keep these tracks together. I now have 2 separate video and audio files of equal length.

Has anyone else had to deal with these? If so, what was your solution? I would like to view these commentary tracks as intended on the disc.

[TheDreadPirate]

AFAIK, there is no way to do this.