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I've finally given up not using Calibre for library management and I've been loading my books for the last two months. Like others have said load the books in small chunks and clean up the metadata and covers as you go.
Make use of custom columns and Virtual Libraries and read the manual. It has lots of useful info and examples to allow you to organise you library how you want. And check the settings in the Tweaks option in Preferences.
And last, but not least backup regularly. This is probably the most important thing you should do.
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