Batch add audio to video - Adobe?
Using FFMPEG the command would look something like this:

ffmpeg -i &lt;sourceVideoFile&gt; -i &lt;sourceAudioFile1&gt; -i &lt;sourceAudioFile2&gt; -map 0:0 -map 0:1 -map 1:0 -map 2:0 -c:v copy -c:a copy &lt;outputVideoFile&gt;


Basically you're taking the source video file and multiple audio inputs, then mapping multiple audio files to the output's audio stream 0. Using -c:v copy and -c:a copy, you arent doing any encoding, so your file will keep its original quality.

That command was taken from the link below, which has more instructions:

http://zoid.cc/ffmpeg-audio-video/

Edit: Forgot to mention the point about wanting to do it in batch. Use the link below to create a bat file in Windows that would target all the specific types like *.avi (or all types using .). You'd want to replace the ffmpeg portion of their bat file with the above. Since you have one audio file, try something like:

for %%a in ("*.avi") do ffmpeg -i "%%a" -i  -map 0:0 -map 0:1 -map 1:0 -c:v copy -c:a copy "%%a"

You might want to back up your files and make a copy elsewhere before you process them, because the above will overwrite them I believe.

Link to that below:
http://forum.videohelp.com/threads/356314-How-to-batch-convert-multiplex-any-files-with-ffmpeg