How to compress .m2v and .aiff into a new movie

I need to compress a large library of videos (1000+ movies) into several smaller versions for the web. The source movies were created using the DVD settings from Compressor 2 and 3. Therefore, for each source movie, I have two files: .m2v for video and .aiff for the audio.
What I want to do (but what does not work): I want to drag the two corresponding .m2v- and .aiff-files of each source movie into Compressor 3, then assign three settings for the web (big, medium, small) and hit "Submit". The result would be three nice video files. (I would then try to automate that workflow.)
The problem: Compressor 3 handles the two source files (.m2v and .aiff) as two separate jobs. But I want them to be combined into one job, as a video track and it's audio track. The resulting three videos should have both video and audio, obviously. I don't want to combine video and audio using QuickTime Pro for each of the three resulting videos, if I can avoid it.
Has anyone ever tried this? Any suggestions?
(My english is not very good, I'm from Germany.)

Unfortunately, you'll need to use QuickTime Pro.
Compressor doesn't combine streams.

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