There is no magic shortcut to getting your series metadata perfect, which seems to be the gist of how I read the OP. Yes the metadata sources contain a lot of crap data, and if you hit ctrl+D on a large series you are almost guaranteed to get a combination of at least two different series names, some duplicate numbers plus a bunch of books with no series at all
What I do is use websites like FantasticFiction.co.uk to get the "correct" series information. I use the Calibre GUI plugin "Search the Internet" (see the sticky thread) to right-click lookup the Author on that website or others like Wikipedia, and then manually overwrite the series column values.
Once your metadata is cleaned up within Calibre, then you have various options for naming the output files as theducks has given you.