@edeniz,
The preferred output for FanFicFare is epub because it can be updated when new chapters come out without downloading the entire story again.
The output_css setting for the [epub] section is used to create a stylesheet.css file inside the epub that all generated xhtml file include. If you think that isn't working correctly for you, please post an epub (generated by FanFicFare), the relevant part of your personal.ini, and what you see wrong with it.
I stopped using Sigil some time ago because it didn't support subdirectories inside epubs correctly. Calibre's 'Edit book' feature is preferred, IMO. Converting from HTML to epub using Sigil, you're on your own.
Re: AO3 extra series, what are you trying to add or ask? And please provide an example URL to a story with more than one series. I don't have stories with every different quirk at my finger tips.
