Originally Posted by Wordsworth
Yes I know exactly what you mean. I tried syncing my Kobo with Calibre and the folders were transferred. I deleted them and just copied the epubs to the reader. Not too certain if epubs would have shown in reader library as they were tucked inside authors folders. With Calibre being such a sophisticated app I would be surprised if there wasn't a way round this. I've yet to find it though.
You are talking about two different things: how calibre stores books in its library, and how books are put in the reader. The former is fixed. But, the latter is not. You can configure the directory structure and file name when they books are transferred to the device. This is done on the device driver configuration in the "Save template" field. The default is to use the author name as a directory and the title and author name for the file name. The Kobo devices are happy with this and allow multiple levels of subdirectories.