I've recently run into a similar issue. I've begun to create pdf books customized for the 6" size of my Sony Reader, and they really look beautiful --- even better than the Sony lrf default. I "Add" the books to Calibre, then edit the metadata in Calibre to point to a particular cover to use, and then have Calibre send the books to the Sony PRS505. Everything works great --- except that the cover doesn't get transferred.
Any ideas, Kovid? Is Calibre actually able to do a full metadata edit on an imported pdf?