I save all my books to epub from Calibre first, in folders made from the 'tag' column. I save them in epub format.
I use a ios program called "Filebrowser" on my ipads, and connect to my main computer. Then copy my epubs to it through wifi. You can password protect the files in the app if you want to.
Then I go to the right folder on Filebrowser, find the ebook I want, and click on it and choose "Open in" and it'll show my options on that device. I use Marvin. It'll send the epub to Marvin's library.
Then just open Marvin and select the book and read.
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