There are two configuration options.
Markdown Deck Library Path describes the location of a directory containing
your flashcard decks. This defaults to ~/Flashcard Decks. Any .md files
in this directory will be added to decks with names based on the directory
those .md files are in. So if I have ~/Flashcard Decks/Physics/laws.md,
I'll end up with a Physics deck containing the cards as shown in laws.md.
Ankdown Location describes the location of the ankdown executable. In order
to use this add-on, you need to have also installed the ankdown python package,
which includes a script called ankdown. This will typically go somewhere in
your $PATH. To find it, it may work to run which ankdown after installing
the package.