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What I want as result: a video with the English stream on the front lineout of my soundcard and a German audio stream on the rear lineout of my soundcard.

So far, I extracted the streams with:

mkvextract tracks video.mkv 1:video.h264 2:audio.ac3

...to get the single streams from an .mkv.

Is there a way to merge the two audio streams to the video the way I want to have it?

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That depends on your video file format and possibly if you have a surround encoder. Some file formats provide multiple audio channels that can be configured for different speakers, others rely on a Dolby encoding or similar to provide the speaker information in one audio stream.

Either use a file format that supports multiple independent audio tracks per speaker or use a Dolby (or some other system like MPEG Surround) surround encoder to encode the audio in to a single Dolby (or similar) stream that can be processed by a Dolby (or similar) receiver.

The encoding option would be the best one if you want to ensure compatibility with most players. Encoders are available in most professional quality DVD/Bluray authoring software packages as well as for some better audio software packages. You can alternately get a stand alone Dolby encoder, but licensing fees (1 time) for the encoder apply.

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