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What formats are supported by a device is controlled by customising the Device driver for a specific device under Preferences->Plugins->Device Interface plugins.
As well as controlling what formats are allowed for that device, you can also control the priority order if more than one of the allowed formats exist in your library.
If you try and send a book which is not in an allowed format, then Calibre will ask if you want to convert to an allowed format before sending.
I find that other than some disk space there is little downside to keeping multiple formats of a given book in Calibre. It can be useful if later you plug in a new device wanting a different format as you may already have that format present.
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