Just click the Update button. Just remember that increasing the settings will give better detail, but slower framerate. The defaults are listed in Command Options. Just click on the action, then type the key you want assigned to it. It's as easy as that.
Some setups work better for some people.
Walk wobble will make the screen sway when you are moving, just like in real life. It is recommended to leave the Y-axis checked, unless you like the reversed mouse feel. You can enable Mouse aiming, called Freelook. Only check the Use Joystick box if you have a joystick installed. You can also use the ACT LABS Gun.