One major issue with Calibre and fanfiction is Calibre doesn't understand the concept of books being updated and revised. If you try adding a story with a new chapter, it creates a new entry instead of replacing the old with the new. I've come up with a workaround.
Configuring ffdl:
In ffdl, set the file naming format to %s - %a in the configuration settings. In most cases this is the naming scheme Calibre uses. Occasionally it truncates the story's name.
Updating a story in Calibre:
1. Highlight the story being updated.
2. In the summary panel on the right side of the screen, click the link labeled "path." In the picture, I've circled it in red.
![Image](http://img855.imageshack.us/img855/3867/calibrepath.jpg)
3. This opens the folder Calibre stores the story in. Take the story downloaded by ffdl and place it in that folder. NOTE: Occasionally Calibre shortens the file name so you may need to rename your file to match the name Calibre gave it.
4. If you do any conversion processing in Calibre, do it now.