I save all my Calibre books to files on my hard drive, then use FileBrowser on the iPad, and wirelessly copy them over. You can password protect everything in FileBrowser.
Then when I want to open something, I click on the three dots at the right of the file, chose "Share File" and it'll bring up message, mail, dropbox and what ever epub readers I have loaded at the moment. Chose your favorite, and it'll send that file to the chosen app. I use Marvin right now.
If you've got the space, you can store your whole library on it that way, and have it as an emergency backup.
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