Originally Posted by GRiker
Using calibre to transfer books to a connected iDevice sends them to iTunes or iBooks (ePubs and PDFs). If you want to send books to Kindle for iOS, you need to drag the books from calibre's library to the Kindle for iOS document sharing folder in iTunes.
If you're talking about a hardware Kindle, there's no conflict between sending books to the two different devices. You can only have one connected at a time, but you can send whatever books you want to either device, as long as you have the appropriate formats available.