As far as I can tell there is no way to do it from the panel. Also you can’t customize the multiview and you can’t rename sources (unless I’m REALLY missing something).
But the software panel works well for all the settings.
I know it’s on old thread, but let me chime in to say that I had Media encoder CS5.5 that was refusing to open and refusing to encode anything from premiere. I deleted the watch folders.xml as recommended above and it worked like a charm. thanks. Just trying to document for the next person who comes along.