Calibre is a black box program and follows Apple's philosophy of you don't need to know where your files are stored. When you add a book to Calibre, a copy will be stored in Calibre. When you convert, the new format will also be stored in Calibre. I believe when you send the book to your device, your book will go to the default location for your device.
If you really need to know where your book is stored on your comp, select a book. On my version (0.7.40), the book cover is shown on the right. Below that, it lists the formats I have converted the book to, any specified book description, tags, and a click to open path link. The click to open link will take you to the Calibre directory where your book is located.
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