Lots of varied advice in the thread. I would suggest you choose a software first, then find recommended naming for it. Many will do some organisation for you, or even let you define the structure.
I don't like calibre, but it's undeniably the most complete solution. I'm not a fan of having to remote into a desktop for certain actions that given frontent doesn't support (there are many).
Some other options: https://selfh.st/apps/?tag=Books