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I am assuming that you are taking about multiple formats of the same book...
Add a book to Clibre, click on the Edit Meta data button and on the top right you will see the available book format... click the icon that looks like a book with a + on it and you can select the other formats of the same book to add...
The program stores all formats of the same book in the same directory and Calibre know what reader supports what and send the right one. There is also a titny arrow on the Send to Device button that bring down a menu and you can choose the format you send to the device.
What I dont know is what Calibre does when there are more than one format supported by the device. Ie, mobi, prc, azw for the kindle or LRF, LRX, PRF for the Sony... Maybe someone that knows more than I can answer that one...
For the 3rd part, I kinda answered as to what I do for multiple formats. I have a Kindle and Sony in my household and keep several formats ready for most books also and what I said above is what works for me though your mileage will vary...
-Rob
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