If everything ends up being stored in the cloud, you won't need to install anything. That may or not help. I've got one or two hundred books on my Kindle, I just know that there is something for me to read on there.
With access to a decent book server you'll have access to millions of books, you already do of course, but the connection to your reader is a bit tenuous, with a stronger link, the books might actually feel as though they are on your device.
I would suggest formatting your reader and starting again, but a bit slower next time.
