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Moved to correct forum.
Short answer: Make sure you don't plug in both devices at once. Calibre will do the rest.
Long answer: You can customize the formats and their precedences over one another in the devices' plugin (see preferences->plugins->device interface plugins). Make sure that you only connect one device at a time. Calibre should then recognize the connected device, and if you send books to it, it will automatically select the most appropriate format according to the settings in the plugin. If no acceptable format is present, it should ask you if you want to automatically convert the book.