Your folder problem is with
Calibre, not with your device.
By default,
Calibre will put the books into folders by author name. To change this, go to your
Calibre preference, and choose
Sending Books to Devices under
Import/Export. If you just want the title listed, under
Save Template change the string value to
{title}. Mine is set to
{title} - {authors}, which is how I prefer my books listed.