hmm...
Well, what you thought of doing certainly would work. Basically, what you're saying is that you have a crap ton of ebooks and don't want to swim through them all to find what you want.
Though I don't personally have thousands (or even hundreds) of ebooks and so don't have that problem yet, I figure that what
I would do, though, is to store my library of ebooks on my computer/laptop and upload only certain ones I wanted to my eBook Reader as needed, rather than searching through a stack of cards looking for the right one.
I use
Calibre to manage my ebooks, and figure you might find it useful, though I started using it for a different reason.
My wife reads fan-fiction from fanfiction.net, and I found a site that can download whole stories from there with little effort. However, the person who runs the site has options to download in HTML, ePub or LRF format which means I needed an ebook format converter so the Kindle can use it. Calibre happens to do that rather well it seems. However, it also tries to act as a library of sorts, keeping all my ebook files together in one place on my computer, which is a plus. (It doesn't break DRM on ebooks. I use a Python script for that, which is a seperate thing.)
You might find Calibre useful as a way to backup your stuff, even if you still use memory cards anyway. The website for it has an
intro tutorial for it that makes it easy enough for a three-headed monkey to understand.
EDIT: Oh, and it's free.