Kindle DRM is device/app specific. If you want to read on your device, you will either need to DeDRM or download via your device (that you want to read on).
The filename is the Amazon ASIN. Handy Amazon shortlink to products: http://amzn.com/{ASIN}
Note that the file contains metadata already, including title/author/publisher and mobi-asin (which is ASIN, but since they are country-storefront-specific Kovid decided not to use ASIN identifier which provides a link to the .com storefront.)
calibre leaves the file alone, with the current metadata intact, and stores its own metadata in the db -- however, when sending to device, that metadata gets embedded within the book. This is not a problem with DRM books, as only the ebook resources are encrypted, not the metadata.
I don't claim to be the "best practices", but here are my ideas and overall basic workflow.
A good default format is whatever the source format was.
It contains all the info that goes into the new formats.
Any Amazon-sourced book will either be MOBI/AZW or AZW3, so keep that. You'll know which ones those are because they will have the mobi-asin identifier.
Since that is most of MY books, I leave them alone otherwise (in fact, my library name is "Amazon"
).
A book sourced elsewhere will either be an ADE EPUB, or be without DRM, in which case you will probably get a choice of formats. Use the EPUB as your master copy. It is superior to MOBI which doesn't support a lot of stuff and doesn't even use css (if you ever edit books this is a nightmare, also conversions will be cleaner) and equivalent to AZW3 except AZW3 doesn't use internal filenames.
I usually tag these "ADE" and "Open EPUB". (Personal preference, you may wish to do so too, or not. Your choice.)