I'll take a crack at the rest of your question, but I'm not a Nikon guy, so I may be spouting nonsense.
Your light meter is what the camera uses to determine the exposure for a scene. It looks at the light reflecting off of your subject and determines whether your shutter speed, ISO, and aperture settings will work for a properly exposed picture.
I think handicap18 has answered that. You might also see it in non-manual modes when you are using your camera's auto-bracketing or exposure compensation.
When shooting in manual exposure mode, you use it to to see when you have the exposure set "properly".
One thing to be wary about is that the meter can't tell the difference between a brightly lit black object and a poorly lit white object. It assumes that everything is grey. When it sees something white, it thinks that it is really brightly lit grey and it lowers your exposure to make the white look grey. When it sees black, it thinks that it is poorly lit grey and increases the exposure to make black look grey. You fix this by guesstimating how darker or lighter than grey your subject is and adjusting your exposure to match. With manual mode, you just directly adjust your exposure. With the auto-exposure modes (aperture priority, shutter priority, or auto), you dial in exposure compensation to correct.
You can also use your meter to check the different light levels in your scene. To do so, you would switch your camera to spot metering mode. You would then meter off of the brightest thing that you don't want blown out and the darkest thing you don't want lost in the shadows. That tells you the dynamic range in the scene. If you compare that to the range your camera is able to capture, you can tell whether or not you can properly expose the entire scene. If you can't, you either have to add light (flash or reflector), take light away (shade, gobo), or take a series of shots for use in an HDR composite. Alternatively, you could decide what's more important (the shadows or the highlights) and just set your exposure to capture those.
That's a whole lot of technical sounding mumbo jumbo. You really don't need to worry that much about it. While you are learning, I suggest that you let the camera handle the exposure (use aperture priority, shutter priority, or auto) and just check your histogram after you shoot. If it is hitting the left edge, use exposure compensation to boost your exposure. If it is hitting the right edge, use exposure compensation to lower your exposure. If it is hitting both, you have a scene that you camera can't handle. Take a few shots at different exposures and keep the one you like the most.
If you shoot in RAW, you can recover from missed exposures a little better. It's more trouble to work with, but it gets you out of more trouble.
