There is a switch in admin to set safe mode on or off and convert the filesystem but you should only set it to on is safe mode is on otherwise use the normal filesystem.
As far as you ftping images and uploading them they will always appear in your folder as you saw this is how we know where the photos are.
So if I understand what your asking there really is no issue here. Your trying to store files differently then the program is meant to operate. All Users files exist specifically in their own data folder nowhere else. Each user has their own directory.