Its all a matter of common sense:
1) Any scene is composed of different elements. Not precisely specific elements but of the nature of them. That is, elements that move or not, how bright or dark they are (and in relation to each other) and how far or close they are (and in relation to each other).
2) Depending on "elements" composition, you may well opt for depth of field (controlling via aperture how many from closer to farther elements you want if focus), or may opt for "movement control" (controlling movement through shutter speed).
3) No scene is perfect, then this is where aperture and shutter combinations come into play. You can get as many different aperture/shutter combinations that give you exactly the same amount of "light" hitting the sensor, but results will differ widely on how the "elements" are pictured.
4) Of course, the light metering is one big issue. where to meter? Remember that the camera sees "everything" as if it was 18% gray reflectance. Your judgment comes into play here deciding if your "scene" is brighter or darker than the supposed average of 18% gray. Think about this: A black cat on a coal pile and a white rabbit on snow. Both receive the same amount of light but your camera will measure either very different than the other. What to do? Use your judgment and experience to shift the exposure value accordingly.
Some matrix metering systems do consider this differences and try to adjust accordingly. Pentax is know to always keep highlight detail, thus "underexposing" scenes where there are highlights.
There are some reference books out there that can help you a lot, like
Amazon.com: Understanding Exposure: Bryan Peterson: Books. Others here may suggest further reading.
Robert B