The Options / Settings

Configure it as you like to

Here at least you need to setup the location (aka directory) where the PdfScanManager shall keep an eye on for new PDF documents. 

In fact you can set up 2 locations: Inside an arbitrary folder and in your "My Documents"

Keep in mind, how you set the "File-name filter" related to the output of your scanner or fax system.

If you put in here "*.*" it will work in every case, but it will also put every renamed document (that you have already processed) again in the Todo-List, if you did a "Simple rename" or "Rename and mail".