Here's what I do. I use Calibre to sort and store my ebooks, then save them to a separate file on my hard drive. Every time I get new books, I save an epub copy in that separate file. That's the file I save to the cloud, along with family pictures.
I have "FileBrowser" on my iPad, and connect to my drive through wifi. Then I can copy files from one to another, or even sync them automatically to FileBrowser. Once they're loaded I can click on an epub and Filebrowser will ask me what app I want to open it in.
I can use any of the Marvin's I have, Bluefire reader, and IIRC Mapleread and some others. Then the app opens up and the book is there to start reading. (Some apps may have extra steps once the app opens.) You'd have to experiment with the apps you already have.
As for sorting and finding them, FileBrowser can search for words in the titles in files and subfiles. I have enough room, so the books are always with me, no cloud needed.
I save in epub, in folders based on the tags, so if I want to browse a genre they're already filed that way. And as for series, I gave up on the Series column in Calibre being useful years ago, and put the series info in the title of the book while in Calibre. I don't even have the series column visible.
That way, when I save the book, it's already in series order. I Do Not Care about the book title so much as it's series placement. So, those copies, outside of Calibre, look like...
[Series Name 01] - Book Title - Author
[Series Name 02] - Book Title - Author
[Series Name 03] - Book Title - Author
With prequels given "[Series Name 00a] - or [Series Name 04b] - " So they'll sort in order. I can still search for a keyword in the title, but they'll sort together in that folder.
If you use the Series column, think you could do this through Calibre by adjusting "Preferences -> Saving Books to Disk", but I haven't played with that much. I'd just rather have Series+Title all as one piece of information.
Filebrowser can be password protected, so you can lock up the files even if someone gets your iPad open. I liked it so much I got the Pro version.
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