Are we talking about metering ambient light or flash/strobe?
A light meter is a tool, just like a camera...there isn't necessarily a right or wrong way to use them...that's why photography is an art form.
In basic terms, you can use a flash meter to measure the output of the flash/strobe...usually you will meter it at the location of your subject. This is important because the light falls off over distance. As Garbz said, a photographer will commonly meter different lights separately, in order to come up with their lighting ratio, you can then take a reading with all the lights, to give you the aperture that you would set the lens to.
If you are metering ambient light, you can take a reflected or an incident reading. Just about every modern camera had a 'reflected' light meter...it meters the light coming off of the subject/scene and gives you a value to expose that at 18% grey. Because different colors & tones reflect light differently, a reflected light reading will often need to be compensated for...this is where you would adjust the exposure compensation on your camera.
Usually, an easier way to meter ambient light is to take an incident reading. In this case, you would meter the light falling on the subject, rather than the light reflecting off of them. Because you are metering the light before it is affected by the reflectivity of the subject, you don't need to compensate for that...you just take the reading and set your camera to those settings. And of course, adjust your exposure to taste.