When you select a folder within the Upload Multiple Files dialog, all images within that folder, whether within the root of the selected folder or within sub-folders of the selected folder, are uploaded into the File Manager folder that you chose.
Only files are uploaded, not the folders that they are associated with. So if you select to upload a folder that has sub-folders containing images, all of those images will be uploaded into the same location within File Manager.
For example, I have a folder on my computer "MySiteImages". This folder contains two sub-folders: "Navigation" and "Ads", each of these folders contain images.
When I open the File Manager, open the Images folder and select Upload Multiple Files. If I then select the folder "Site Images" and select Upload, all of the images within the "Navigation" and "Ads" folders will now be listed together in the Images folder on my site. The folder structure of the "Navigation" and "Ads" folders is not uploaded.
To maintain the folder structure you have on your computer within your site File Manager, first create the top level directory if applicable (MySiteImages) and then within File Manager create the folders that you need within that directory (Navigation and Ads). Use the Upload Multiple Files option to upload your images in each sub-folder individually.
