From what I can figure out there is no really good library available for ebooks. You have to show them all, and cannot file them easily or readily into files or folders. Particularly if, like me, you happen to be somewhat inept with the world of computers, programs and the associated jargon.
I find Calibre good for what it does but it is limited.
To solve the problem as best as I can, I use a program called Book Collector. At least it keeps all the books in whatever field you choose say, format, author, etc, and can be sorted how you like at the touch of a button, say read or unread. It also has the added delight of showing the covers. It can upload almost all metadata from a huge variety of inbuilt sites. Of 176 books I have loaded into it there are only two which I had to manually load the data.
The current drawback is linking each book directly to the reader. This is possible, but I just haven’t got around to it yet, mainly because I am slightly unsure of how to go about it.
The link is
http://www.collectorz.com/
it is not free
Hope this helps,
John