Needlehawk is correct. There is no "calibre format" ebook. The calibre software simply acts like a file management system and a card catalog, combined together. There are lots of extra features, but when you simplify it all down that is calibre's real function.
When you add a book to calibre, it keeps the book in the original file format - it just makes a copy. If you need a different format, calibre can covert the book on demand. As to the "best" format to keep books in (and possibly deleting all others)... all of the existing ebook formats have slightly differing features and implementations. So there are substantial differences between ebook formats of what features are allowed. Some cannot handle images at all. Others don't allow drop caps, margins, alignment (centered, justified, etc), font faces, font size, etc while others do. Basically ebook formats are like HTML v2.00 - it's pretty good, but woefully short of being able to mimic what can be done with full-color printing and professional layout.
Having put all your books into calibre, you can delete them, but it is suggested that you always keep two back-up copies of any and all computer data in case of catastrophic failure. Disks (cd, dvd, blu-ray) are not always viable over time; HDD are actually a safer option. But for safety this means having at least two off-line copies (1 disk and 1 HDD copy) just in case. Overkill, but better safe than sorry.