Originally Posted by Agama
PeterT has given you calibre's command line interface (CLI) syntax for achieving your requirements.
If you are using calibre's GUI rather than CLI then you cannot get the conversion output to be saved directly into a single folder.
However, you can use the Save-to-Disk function after conversion to save the books to a user-defined folder structure by using the template found in: Settings > Saving books to disk.
After saving as per Agama
's suggestion, you can delete the mobi's from the Calibre book folders by selecting all the books and using the Remove->Remove files of a specific format from selected books...
Its a good idea to backup your library before doing bulk operations such those suggested, then if you make a mistake you can start over.