Like andygates I do most of it by folder - I use Calibre for storing and things, but for reading I like to keep things organised differently.
I store all of my books on the SD card in case I accidentally cause some form of reboot loop while I'm messing around with the reader, that way I can reflash the device without losing any of my books, or the associated metadata - e.g. the last page I was on with the book.
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