Digital SLR photography allows you to control how light is exposed to your camera's sensor. In manual mode, you are given control of ISO, aperture, and shutter speed. The way that these three elements interact with each other produces your photograph.
ISO is the camera sensor's sensitivity to light. Lower values are less sensitive, whereas higher values are more sensitive to light. With a low ISO value (e.g. 100), your photographs will look clean (without camera grain). ISO 100 is recommended for a sunny day. With a higher ISO value (e.g. 1600), your camera will introduce undesired noise and grain. In low light settings, using a high ISO value helps you get your desired shot.
Aperture measures the amount of light that the camera lens lets through. Lower aperture values (e.g. f/1.4) correspond to more light, while higher aperture values (e.g. f/5.6) allow less light to pass through the lens. In addition to the amount of light, aperture also controls the amount of blur for out of focus areas. Lower f-numbers produce more blur, whereas higher f-numbers keep more of your photograph's detail.
Shutter speed controls the amount of time that the camera sensor is exposed to light. Slower speeds (e.g. 1/30) allow more light to be captured, while faster speeds (e.g. 1/1000) reduce the light that is exposed to the sensor. Slower shutter speeds can help portray movement, and faster shutter speeds can be used to freeze a moment in time.
Understanding how these three elements play off of each other is important for capturing the photos that you want. Is it dark? Use a higher ISO, larger aperture, and a slower shutter speed. With practice, you will grow a better understanding of what settings to use.