Auto-add is handled by the calibre GUI (like, the main program)

not the server.
If you want to run the GUI unattended in a scipted manner just to auto-add books, you can also simply use:
Code:
calibredb add --with-library=/path/to/library/ --recurse /path/to/scripted/add/folder/
Repeat as needed, with whatever combinations of libraries and add folders.
Alternatively, you can specify the environment variable "CALIBRE_CONFIG_DIRECTORY" and start the GUI and manually configure auto-add folders and default library for each config_dir, then script it to start up and shutdown at regular intervals... but I prefer my method above.
Yep, there's lots of cool stuff you can do via the command-line, in the finest unix tradition you can do practically everything with fine-grained control using the cli.

For even more options, see:
http://manual.calibre-ebook.com/gene...cli-index.html and the calibredb command particularly.
Welcome to MobileRead, and welcome to calibre.