Howdy! Are you familiar with the way WP multisite stores its sites in the database and not in the file system? Or are you wondering where the media files are?
Sites in multisite don’t have a folder in FTP. When you create a site in WP multisite (or clone a site with the cloner) and have something like
mydomain.com/mynewsite
WordPress automatically maps that to specific tables in the database.
The media files for that site will be found in a different location depending on your original version of multisite.
/wp-content/blogs.dir/## [for installations that started before 3.5]
/wp-content/uploads/sites/## [for installations starting with 3.5]
The ## is the ID of the site which you can find in wp-admin/network > All Sites by hovering over the site name and looking at the ID=## in the URL.
