If you select a remote folder when connected to a remote server with NotePad++ and NppFTP you can right-click and create a new directory. But I don't see any way to create a directory inside of the directory you just created. If you double click it to select it and then right-click, the Create new directory link doesn't seem to work. It looks like a folder has to have already have content before you can add more.
Am I missing something?