[JimmyR]

I think ringy is using ">" as a path separator in his post, not as actual characters in the filename. His template seems ok.*

Adams, Douglas/Dirk Gently/01 Dirk Gently's Holistic Detective Agency.epub

Edit:

what I would like would be:
Adams, Douglas>Dirk Gently>01 Dirk Gently's Holistic Detective Agency.epub

This point is moot since it doesn't change how Calibre saves files to the library but, the template should be:
{author_sort}/{series:||/}{series_index:0>2s||} {title}

{author} instead of {author_sort}