This is an absolutely superb post. I now have Calibre managing my Kindle. I transferred all my old ePub books to the Kindle, created a custom column for the Kindle collection names, populated it from the Kindle, tidied it up, and assigned all the new books a collection.
I found it very useful to restrict my model to one collection per book. So, my latest purchase sits in "new books", when I start it it will migrate to "bedside table", and when I've finished it "Fiction - A to H". I plan to essentially maintain the collections on the Kindle, repopulating my custom field in Calibre from time to time, and using Calibre for big updates, like a spree in the sales.
I can see there are 1,000,001 ways of exploiting all these features, but that's the one for me
Thanks for all the tips contained above. Donation in the ether.
amjb