5.1 mixes with Goldwave and the voice-over plug-in are possible... but it takes a little extra effort. In short, here's how I've been doing it:
1) Use BeSweet to convert the demuxed AC3 file to six mono WAV files... one for each channel (FL, C, FR, SL, SR, LFE).
2) Using Goldwave, match the volume of the RiffTrax WAV to the center channel mono WAV to normalize the riffs and the movie dialogue.
3) Use the GW voice-over plug-in to mix the new RiffTrax WAV into all six mono WAVs.
4) Use BeSweet to recombine the six mono WAV files into a new AC3 file.
All six mono WAVs will need to have the voice over plug-in run on them. For the channels you want the RiffTrax to play through, mix as usual. For the channels you don't want the RiffTrax to play through, turn the voice volume control of the plug-in to the off position. This will cause the movie audio to still lower during riffs, but the riffs themselves will not play through those channels.
For example... what I usually do is to use the voice over plug-in to mix the RiffTrax audio into the two rear channels (SL & SR). Then I use the voice-over plug-in to mix the RiffTrax audio into the other four channels with the voice volume turned off. All six channels will lower during the riffs, but the riffs will only play from the rear channels. This has the effect of making it sound like the riffers are sitting behind me. It's pretty cool.