As I've mentioned before, the process of designing a book jacket is largely beyond the author's control (especially if you're a debut or mid-list author) and you'll have relatively little input. It's unlikely that a cover you absolutely loathe will be selected, but it does happen and you'll need to keep the lines of communication with your agent (and, by extension, your editor) open so that any problems you might have can be identified and dealt with as soon as possible.
There are a few systemic problems in the art of cover design that invariably rear their ugly heads (for instance, the fact that they are occasionally super racist), and in the event you encounter one of these issues, I strongly suggest you talk to your agent and editor immediately. A bad cover may hurt your sales but probably won't seriously damage your career; a brouhaha over a racist or offensive cover could be a total disaster. (There is such a thing as bad publicity.)
On the e-book front, it turns out the cover question is a little more complicated than you might think. I generally find Motoko Rich's e-book articles douchey and annoying, and while this one is no exception, it does elucidate some of the issues endemic to e-publishing (namely, when you're reading your Kindle or Nook in a public place, no one can see what you're reading/how high fullutent you are). This doesn't spell the end of the flashy book cover, however: as the article itself notes, these covers 1.) are still used on the print versions of the books, 2.) are effective at catching the eye of both e- and p-book browsers on websites like Amazon's, and 3.) will be just as (if not more) effective in e-venues like Facebook or the iBookstore as/than their print counterparts are on store shelves and in subway cars.
What do you think, gentle readers? Are you as enamoured of e-book covers as you are of the "real" ones?