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The idea with Calibre is that it's a book database, with all of the managing to occur within Calibre. As has been noted, Save to Disk allows you to save in the directory structure of your choice. In your example, you could tag bills, receipts, letters, etc. and then choose tags for your Save template, so that bills went in to the Bills folder etc.
Having said all of this, Calibre is designed as a book database, so will work better for organizing your books. Just don't try to look at or use Calibre's directory structure. If it offends you, tuck it away where you don't have to see it. Access your files from within Calibre and Calibre will manage them well.
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