Using WP Smush Pro for lots of images - while still local

Hi - I'm a photographer and have tons of images - have not uploaded to the media library as there's no way to put them in subdirs (when will WP add this?) 9some of the images may have the same name but be totally different based on the dir they are in), and I'm mainly using slide shows, so I've been using WOWSlider which allows me to upload to directories of my choosing and then access them with a shortcode in the post or page. Can I shush my images using WP Shush Pro locally before final deployment of the site to my server? Or do the files have to be in the media library. See my regular site here - am working on my conversion to WP - BurleighPhoto.com
Thanks for any help you can give. Craig.