There are several things going on here, I'll break them down.
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Originally Posted by deleteriousone
Science Fiction\Anthony, Peirs\Adept Series\ Adept Series 01 - Split Infinity.lit
Science Fiction\Anthony, Peirs\Adept Series\ Adept Series 02 - Blue Adept.lit
. . .
Science Fiction\Anthony, Peirs\Incarnations Series\ Incarnations Series 01 - On a Pale Horse.lit
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With a directory structure like that, you can read the series, series_index and title from filename. See theducks answer.
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to recap I want Calibre to store files as genre\author (last, first)\Series\filiename including series number\
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This may be a mistype on your part, but you don't get to decide how Calibre stores its books at all.
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It seems with such a powerful program having the author's listed as last name , First Name would be easy. For me at least it is not.
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If you're still building your ibrary and have only a few Authors in it, it is very easy: Go to the tweaks section of the preferences and find a tweak called "author sort name algorithm". Set it to "copy". Save and restart. Now, fill in your authors as LN, FN. If you have some books already added to the library, in the tag browser, right-click on an author and select "manage authors". Make sure that the authors you have show as LN, FN the way you want, then hit "recalculate author_sort values".