try this for metadata from filename and check if get metadata from only filename is selected
(?P<author>.+?) - (\[(?P<series>.+?) (?P<series_index>[0-9]+)\] - )?(?P<title>.+)
Are you talking about the file saved inside calibre on adding to calibre
or when you are using the save to option
For save to I personally use this as I dont want to have each book in its own folder in my reader
{authors}/{series}/{series_index:0>2s}. {title}