@Andrew85: simply open the app, scroll until you see the button "nowatchdirectory", push it, push add, select the directory you want to keep unread.
Maybe you could need to reboot.
I use it for music I don't want to be indexed in the media player, and it works well.

EDIT: the program from its menu offers also to "rebuild databases" and this should allow you to refrain from rebooting.