Graham,
I organise the exact same way. If I need to find cover art, I do it manually. ie. hit Amazon, search engines, discographies etc.
I'm slowly going through my old vinyl stuff, and I find it a pain to scan LP covers in pieces and stitch em together.
Mostly I can find good quality CD covers for these albums.
The only exception is the more rare, non-mainstream records which I have a few of. These I scan, stitch and patch up as best as I can.
I've never really used the automatic way of getting cover art.
Not that I don't trust it to find the right cover or anything...