Both Calibre and the Kindle product line handle this extremely easily. As long as the books that you're trying to transfer onto the Kindle don't have DRM encryption within them, it's the simple act of plugging your Kindle device into your computer, waiting for Calibre to recognise it, and then clicking the big "Send To Device" button which will appear. If your books are not already in the correct format for the Kindle (which takes the .mobi and .azw formats), Calibre will ask you for permission to 'convert' them automatically - you just need to accept!