When you upload your movie to YouTube (or a similar service), it will be processed for use on their site. Here are some tips to ensure your audio survives the processing:

If you are recording both Mac audio and a microphone, your movie will contain two separate audio tracks. YouTube will strip the second track, leaving you only with the Mac audio.
The workaround is to "flatten" the movie, combing both audio tracks. The easiest way to do this is to export the file again using QuickTime Pro. If you don't already have QuickTime Pro, Apple does charge $30 for it.
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