http://manual.calibre-ebook.com/faq....tory-structure
If you want to keep your books in the folder you had, you must use the command-line method described here:
http://manual.calibre-ebook.com/cli/ebook-convert.html
If you want to use the library interface in any way, shape or form, you will have to allow calibre to organize the books for you. @Worldwalker has
an excellent explanation here why that might not be such a bad thing...