I guess I'll throw in my method.
I use only 2 programs to make my Rifftrax DVD's, Nero 6 and DVD Decrypter.
First I pay for the DVD and the Rifftrax (I sell the DVD later)
I unzip the Rifftrax to the folder where I keep them.
I decrypt the movie to my hard drive into its own folder.
Next I start Nero 6 and use the program that converts DVD's to mpeg4. Nero does an excellent job of identifying the main movie title, which is all you really want, filtering out menus, special features, other audio tracks. The program also reprograms the mpeg4 file to fit on a regular sized DVD. This takes about as long as the movie plays. I have never had a problem with the audio getting out of sync with the video using this program
Next I go to the "make movie" feature in Nero 6. I import the unzipped Rifftrax and drop it down into the audio container. I then play the rifftrax and pause the audio when Mike tells me to. I then make a segment cut and delete the rifftrax intro. (Don't worry, the original rifftrax remains intact)
I then bring in the mpeg4 movie file and drop it into its container. Using the grab feature I can adjust the audio rifftrax to sync up perfectly by shifting the audio track back and forth in its container if it is out of sync. I adjust the movie volume to be just below the Rifftrax volume. Nero does a good job of equalizing the volume so there are no loud or soft variations after you get the volumes to where you want them.
I then use Nero 6 to add chapters automatically, create a menu screen and then burn the DVD.
It takes a little over 4 hours to do all this if its a 2 hour movie. I am very pleased with the results