I've found a quite easier way in OS X using Quicktime Pro. All you have to have is the digital copy of your movie, the mp3 of the Rifftrax, Quicktime Pro, and a few minutes to edit, and your done, with no encoding or anything. This is of course only good for a digital copy, encoding it to DVD would result in quality loss. But honestly, it takes no more than five minutes to do once you have everything you need.
Would anyone like to me post a tutorial, or does this infringe the rules in anyway?