There is no way in Plex to say: “Always pick the second audio stream in all episodes”.
If the files are already in mkv format, you can use a batch file to set those languages in all of them at once: How to remove tag spam and set language in several MKV files at once
If those files are in a different container format, you could use yet another batch file/script to remux them to mkv all at once, in preparation for the above.
