Do you have access to the server ? I mean, not through the console, but with FTP access or a distant desktop ?
If so, you can create subfolders in the 'res' folder. These subfolders are accessible with the HTTP access to the 'res' folder.
Another way should be to upload a zip file of your folder with the console (with the xtk:fileRes) and try to unzip it with the ExecCommand function, but beware, this could be dangerous for your instance. I recommend you to try it in a development environement.