Create columns for genre and subgenre in Calibre.
You will find a place to configure the path to save files to under Calibre's device configuration, use something like "Books/{#genre}/{#subgenre}".
At least that's how I would do it. Apparently there is a better (albeit more complex) way to configure it which is documented here:
https://manual.calibre-ebook.com/sub_groups.html
Either way, once you transfer your books to your device they will be stored in a nice directory hierarchy that is easy to access via KOReader.