Okay, if you're wanting to run SMP (allowing multiple CPU cores to process a single WU), you need to download the SMP client:
http://folding.stanford.edu/English/DownloadWinOther
The one you want is the last one listed. Click the Windows logo to download (
direct link), and be sure to check out the
Install Guide and
Passkey information link.
You'll want to sign up for your passkey first - this is most definitely worth your time, because the bonus system is tied to it now. If you don't use a passkey, you'll get a fraction of the points you'd get otherwise. Keep in mind that you have to submit X number of WUs successfully before the bonus kicks in (10 WUs IIRC).
With the SMP client, you will only run a single client. Since you're showing 50% on each core, I'm guessing you're running two standard clients instead. To configure, I'd take a look at the install link posted above. Short version, add -smp flag.