When you are exposing your image manually, you must make your shutter speed, aperture and ISO work together. Usually you will choose your shutter speed or aperture first, based on the situation. For a portrait, for example, you might determine that you want a large aperture so that you can blur the background. You would choose a large aperture and then you would adjust your shutter speed to match that setting. The larger your aperture, the faster your shutter speed should be (most of the time). In well lit situations, you will never need to mess with your ISO. You will simply leave it set at 100 or 200. But, if you are shooting indoors and you cannot correctly expose the image without slowing the shutter too much (making camera shake a problem), you would raise your ISO until you could speed up your shutter.
If you are taking a picture of a landscape, you would need to close down your aperture to increase the depth of field. This would require that you slow down your shutter speed. In some situations you might want to increase your ISO so that you can still hand hold your camera. In other situations, such as if you are taking pictures of a Christmas tree, you would want to use a tripod and leave the shutter open to really capture the twinkling lights.
Let’s break it down again. Let’s assume you are taking a portrait. First, set your aperture to the largest it will go (the smallest number, confusing I know). Then close it back down one or two stops for sharpness (one or two clicks of the dial). Adjust your shutter speed until your camera shows correct exposure. If your camera’s light meter is telling you that you need to slow your shutter to 1/80 sec or slower, begin to increase the ISO until you can keep the shutter speed fast enough to hand hold. 1/120 sec is a good speed to work with for general purposes.