Maybe it would be most easy to just use calibre to manage your ebook collection. A Calibre Library is just a folder structure and all your books are in it. You can't organize these folders by yourself, but calibre is much better to find and manage books than just folders.
If you don't want or can't use calibre somewhen in the future, no problem, all your files are still there. And of course you could always save the library in another structure to your disc, with templates.
To update the Metadata inside the files, you do not need to convert or save to disc. Just use the polish book tool and check "update metadata". Then all your files have the metadata inserted, in case of a database corruption.
You could also open the path to each book in calibre, if you want to manualy copy the file or you could use the save to disch feature. I do not use it, but you could even send books out of calibre per e-mail.
So my advice would be, to just use calibre to manage and save your books. It is easy and gives much possibilities. And is it not some esoteric system, that you are bound to, but all your data is also in the files. Maybe just see it as an better explorer just for books
