I have just reread Diana Wynne Jones's Deep Secret in the 2002 paperback edition with Charles Vess's perfect cover (a favorite author, favorite illustrator). What fun, then, to find this preliminary sketch with Vess's notation, "Irene—I like this idea: the hotel lobby w/ s/f con people (as well as our principle [sic] characters) checking in as Rob the centaur bursts from air. This is a pure white background w/ design elements a la Saturday Evening Post. Charles"
Good illustrators must almost always begin with someone else's story, then find their own way into it to enhance readers' experience. For Deep Secret, Vess helped me visualize Nick, the tall, dark-haired boy in the center, who bears a strong resemblance to Rob, the centaur. (Don't ask; just read the novel.)
What this sketch does is remind us that various degrees of collaboration are involved in publishing. Jacket design has been the responsibility of the marketing department in major publishers; author and designer may never communicate at all (self-publication is obviously different). Sometimes, though, there can be close consultations. Vess has written about the process of designing a cover for Ursula Le Guin's Earthsea and about going from sketch to colored illustration in their complete, one-volume edition of that series.
Sometimes, moreover, the pictures come first. Jackie Morris, for instance, composed a story to pull together a series of her Christmas card designs into The Quiet Music of Gently Falling Snow. Or an existing set of pictures might be paired with a text, as in Ron Drummond's project of decorating John Crowley's Little, Big with existing artwork by Peter Milton. Art is protean and no rule need ever be followed slavishly.