Hi
To copy the books into Calibre. when the kindle is connected you select the device icon in calibre.
Select all the books you want to add then right click and select add to library.
If you want to transfer your collections, your kindle would have to be jailbroken and you would need the coolections manager installed on your kindle.
see the following thread for specific details.
https://www.mobileread.com/forums/sho...d.php?t=186305