HOW DO YOU DESIGN A BOOK COVER?That description applies to just about all design, I think, not just book cover design.
First you start with a blank page, stare and think really hard, drink lots of coffee, take lots of breaks, fix the copier jam, update your Facebook page, get over the fears that this project is the one that will finally expose you as the hack that you are, and then just trust to do what you feel is right from what you've read, present your ideas to find out how they live outside of your head, listen to feedback, try to leave work at a decent hour, have a life, floss, get enough sleep, have a good breakfast and come back the next day to redo it all over again. It's that simple and fun. And if it isn't, then get another blank page and start all over again.
The designs on the site are very nice, too - I recommend you check it out.