If you want to upload there media files to another place in the same instance of IIS, for example a different folder, there are several things you can do.
1) map your other location to the /media folder on your site as a virtual folder in IIS. That will just work out of the box, and all of your existing media files will continue to work if you move them to the location you're mapping to.
2) change the path in the file /config/FileSystemProviders.config, look for the virtualRoot parameter. By default, it's set to "~/media/", but you can change it.