This describes some of the screens you see when running the GUI version of the Folding@Home program (if you decide to run the console version someone else will have to provide examples; I don't run that version.)
When you right click on the System Tray icon for F@H and select "Configure...", the first screen will look something like this:
Of course, you'll have your own name there. Click on the "Advanced" tab, and you should see something like this:
You can change the CPU Usage Percent if you don't want F@H to use all of the available CPU time; however, it runs at a low priority so even if it uses all it can get you probably won't notice its effect. You can also adjust the slider for the Checkpointing frequency to determine how often F@H will write checkpoints to the hard drive. For example, with checkpoints written every 30 minutes, if your computer crashes you should never lose more than 30 minutes of work.