We have included Muse Score within SS as a way of letting people know and use this very good free scoring program. The only integration with MuseScore is that when installed via the Music Docs button of Song Surgeon, it can be opened from within the the Music Docs button of SS.  Other than that you should use MuseScore as a stand alone program. Musescore cannot create sheet music from a standard audio file, or for that matter, can any other scoring program, unless of course a midi file is being used which is not a standard audio file.