Problem solved.
All I needed to do was creating a file on the players root dir and call it .is_audio_player
and put the following lines into it:
audio_folders=Music/ output_formats=audio/ogg,audio/x-ms-wma,audio/mpeg,audio/wav,audio/x-flac,audio/mp3 cover_art_file_type=jpeg cover_art_file_name=cover.jpg
The files are transfered as usual and the cover.jpg gets created automatically!