Thanks for the specifics of what you are trying to do.
My first question would be to double check to make sure you do indeed need to do some of this at all. You say you want to "save to disk to replace the originals" and you want the file structure to "browse as files on PC". Do you have a particular reason in mind why you want to browse via the file structure, rather than just using Calibre? You can do everything you can do in the file system and an awful lot more from Calibre. Why is it that you feel you want to browse books using the file system?
If it is just a "nice to have" rather than an actual tangible need, I would suggest living without it for a while and see how you get on. Maintaining both a file system based directory copy of your books and a calibre library will double your effort to keep things up to date. I would suggest most Calibre users do not bother with a file system based duplication of the files. There is one scenario where it is required that I am aware of, and that is if you have a device that cannot be sent to directly using Calibre, however I believe that is the exception rather than the norm.
The next point you raise is multiple series. There are threads on this forum about how people handle these. Here are a couple for you:
https://www.mobileread.com/forums/sho...d.php?t=121412
https://www.mobileread.com/forums/sho...d.php?t=119522
Have a read through those for some ideas of how to approach it. If you want to use a subcategory type approach in the tag browser, I guess you would have to use a series name something like:
Riftwar Arc.01 Riftwar Saga.Magician [1]
If you don't care about the tag browser nesting, then you could use multiple series columns for the book.
When it comes to "exporting", again it depends on exactly what the destination is and the type of device you have. For instance if you have a Kindle the file path is unimportant, particularly if you only manage your Kindle from Calibre (storing them as by title per author is sufficient), as the Kindle uses the internal book metadata not the physical filename for MOBI files.
On other devices the file path does play a role. You can use the Calibre template language to come up with a file path how you want. Exactly how to do that depends on the decisions you make on how to store the series in the first place.
I would caution you against trying to get too complex/clever as every extra "layer" of columns and series depth levels etc just adds to your maintenance. It also significantly increases the complexity of your save templates and plugboards if you are trying to incorporate all that additional information. You could always add it as you need it at a later date. Get your books in Calibre, with a nice clean set of basic title/author/series/cover/description metadata and a genre. Then look to enhance it when you have been using it for a while. Not only may you find that your requirements change, but remember that Calibre is continually changing as well - the heirarchical categories feature only appeared in the last week or two alone. By the time you find you *really* need a particular feature, there could well be an even better or simpler way to do it.
With that said, if you absolutely must have that file path today I am sure someone can help you out with it, once you have specified exactly how and where you are storing all those elements that make up the series information.