Unfortunately, the answer is most likely no, not with that plugin.
Some plugins and themes bypass the WordPress media system, which also means they will by pass the watermark system.
We do offer a plugin called Bulk Watermark Ultra, which can scan your entire uploads directory and add watermarks to images which are not in the standard WordPress media uploads directories. (note: the features is not available in the free version)
Here is a link: http://mywebsiteadvisor.com/tools/wordpress-plugins/bulk-watermark/