Just use the upload functions from a client. It lets You create subfolders. Don't copy anything manually to the FMServer directories since one has to make sure that the access rights are set for FMS etc. (the upload function does that all for You)
But if the file is already up there, is there a way to move it. From what I understand you are saying, I would have to delete the file from the server and then upload it to the subfolder. Thanks for your reply.