You can change the server path for where uploads from the Skyline driver are stored. It makes good sense from a server management point of view to keep these files separate from other files such as those uploaded via the web portal.
To change the upload directory:
Log in with Host rights and go to Admin.
In the Portals section click Default Configuration.
Find Upload - Directory in the list.
The default upload directory is "Documents\UploadedDriverFiles\". Amend as required.