I vastly prefer it to calibre web personally, but it's all up to personal preference. Kavita has a pretty extensive user guide too

I use calibre to label books by series. I don't think I did anything crazy with the folder structure outside of putting comics, manga, and books in separate directories.

I have one media directory with books / manga / comics in separate subdirectories. I process metadata with calibre or other tools as needed, and point Kavita at my books directory and tell it to scan. Kavita should automatically group books of the same series together provided the series name is exact. (eg: "The adventures of Bob" vs "adventures of Bob, The" would be seen as different series. Kavita should also group the libraries together by directory, so I have 3 libraries, books, manga, and comics.

You do need to make sure books are all in the correct formats. I batch convert everything to epub and limit Kavita to only show epubs to avoid duplicates.

The upside to all this is that Kavita comes with a cleaner interface imho, opds is easier to set up, and I've had less issues with it. Also users can set their own reading lists and collections if you are setting this up for other users.