You can create new folders by prepending to the filename:
Code:
mynewfolder/file.xhtml
Or you can select any pre-existing folders with the dropdown.
Note that creating new folders does not make them appear in the Book Browser. The displayed Book Browser folders are virtual-only. They merely group things by file-type.
Some things to keep in mind are: 1) you cannot move files outside of their virtual Book Browser group. 2) you need to enable the "Book Browser shows full path" user preference to be able to "see" the physical folder structure of your epub.