Closing, please be more specific about what the precise problem is. It's normal for some files to always go in root, and it's possible to change the exporter settings so everything else exports to root rather than a media subfolder.
I imported a font and images (png) in project's folder Files (with Construct 2). In this folder Files, I made subfolders to tidy up a bit.
Maybe I'm wrong, but I understand the "/media" when exported is for these files. But when I export, I've got no /media folder, which means my 250 png and the font (+css) are on root, mixed with application files. It's not really handy when I need to upload a new version, without uploading images.