Are you running one of the F@H High Performance Clients? I haven't tried the *normal* client, so I'm not sure if that amounts to much of a difference. Regardless, seeing 50% CPU usage on a Quad Core is common. I ran into the same problem, and asked about it on the F@H forums. Long story short, the clients are "inefficient" when running on Windows, for whatever reason. Even though I can pull up the Task Manager (Showing Processes from all users) and it lists 4 work units being folded, it runs each at 50% for whatever reason.
If you install a 2nd CPU client into a different folder and run that as well, I noticed it got my CPU usage to 100%. Whether this will net you more points a day or not, I'm not sure. While I tried it briefly, I wasn't happy with my Computer's temperature while running both CPU clients and my GPU client, so I can't comment on its effectiveness, other than it showed a CPU usage of 100%. Whatever you end up doing, I'd say consistency is best. Keeping it running overnight is a good way to make progress, if you aren't concerned with leaving your computer on for extended times, or using the electricity.
For me, F@H never seems to throttle back as much as I'd like when I'm gaming, so I usually just shut off the client when I need to. I believe you risk losing some information when you do this, but I haven't had many issues. Any big dips in my points per day is usually because I sat at home playing games, or I just forgot to start up the darn clients *after* a game
Hope you picked our team for Folding