To control where books are stored on your device you just have to change a template within the device drivers configuration. Documentation on the template is found here
https://manual.calibre-ebook.com/template_lang.html
Since you want all books in one directory your template would start Books/ Then you would need additional bits to specify how to name the actual file. One simple approach would be Books/{title} - {authors} which would include the author after the book's title.
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