Originally Posted by highstream
Yes, that's been my idea so far, since it's so easy to convert and I'm dealing with different kinds of files from a variety of sources. I mean no offense to calibre's developer(s); I'm just more focused on using what's on my Kindle and adjusting that as need be than developing a calibre library or learning its command line structure, which for me will rarely be worth the return (there's always the public library and I like reading and listening to books).
Oh goody, I was right for once
If that is how you want to handle things, then that's fine. I personally think that using calibre is easier in the long term than any alternatives I have seen.
For what you want to do, after the conversion, do a "Save to disk". This will copy the new ebook to wherever you want it. There are a few choices on the menu and some preferences about exactly what to save (cover as a separate file, updating the metadata during the save), so have a play to get exactly what you want. Once you have done the save, you can delete the book from the calibre library. This will remove all evidence of the book and formats from within calibre.