Most of your questions are covered in the Calibre (help) FAQ
http://manual.calibre-ebook.com/faq.html so I won't go into those
First off:
Let Calibre
Manage. Believe it or not, that is it's primary function. Managing formats, metadata...
When you connect your device, Calibre uses the (user configurable) rules for that device. It
knows to send AZW3/Mobi to a Kindle; EPUB to a Sony...
No need to
split formats. 1 book: all formats is fine

Preferences: Tweaks
Take some time to read (don't rush to change, yet) the various descriptions.
These are EXTRA controls for knowledgeable users. Start messing with these too soon and you will be rebuilding your metadata later to undo something you
thought 
you wanted