If you're just looking to manipulate pdf natively Calibre is not the best choice. There are plenty of third party pdf utilities that can do this, you're probably best off with one of those. I can't provide firsthand experience, but I've seen a lot of people recommend Briss:
http://sourceforge.net/projects/briss/
You might be able to integrate it with Calibre's 'Open With' plugin to streamline things...