How to merge two files: video file with stereo audio track + wav-file with 5.1 surround

I have 1000s of video files with stereo-audio.

Now I need to merge each of these files with a new wav-file with 5.1 surround-audio track. These files have same name as the original file with an extension.

Output should be the original video file with stereo-audio (audio channel 1-2) + 5.1 surround (audio channel 3-8).

Is it possible to batch this workflow in Adobe Media Encoder?

As an alternative, I will need to transcode the original files with stereo-audio to files with 8 channel audio where the original stereo-audio will be mapped to audio channel 1-2. The empty channels 3-8 will be filled out by the software which create the new 5.1 surround mix.