Many people have asked "where are the files stored" and the answer is "nobody knows". It's probably in a database rather than as separate files. Yes, you can happily installed and run the "normal" Kindle for PC alongside the Metro app.
To close a Metro app you can use the keyboard shortcut "Alt+F4", although, as on tablets, there's no real need to explicitly close them - the o/s looks after their memory usage and swaps them out when necessary.
Currently proofreading The Poison Belt, by Sir Arthur Conan Doyle.