I could be out of tune here but I am going to assume that you want to learn more about using the Manual Mode in photography. If I misunderstood your concerns simply ignore my comments.

Perhaps using the camera in the Manual Mode is a natural to me because that was exactly what I was doing when I was a youngster. All the cameras available at the time were very simple and only had a shutter speed dial and a manual advance mechanism for film.The shutter button to expose the film obviously, was part of the camera. Exposure meters in camera took some time. The apertures were set in the lens and the exposure depended on a hand held exposure meter that was not super precise at the time due to the measuring cell although that changed as years went by.

What I consider important when using the Manual Mode is first to understand exposure which is simply basic photography. Exposure with digital cameras is not a science and using the color histogram ensures a high proportion of well exposed subjects. We all know that editing software can open shadows in ways we could not ever dream when we were using the optical darkroom to develop and print our film. With digital exposure should ALWAYS be based on the most important highlights to avoid clipping (overexposure) because we all know that once those highlights are overexposed we will not be able to recover details in them.

Since ISO, aperture and shutter speed are set by the operator, so called "exposure triangle," we have to learn what ISO we need according to the lighting, what aperture we want for depth of field and what shutter speed if we want to freeze motion or blur the movement of the subject. For landscape photography under sunny conditions we have learned that a small aperture, like f11-f16 will give us all the depth of field we need to see details from foreground to background. Usually the base ISO of the camera is plenty enough especially if using a tripod.
Because the exposure meters in camera are so sophisticated and precise knowing exposure we know when the exposure needs modification. In the case of matrix, evaluative or multi pattern metering we need to understand that those are computerized exposure meters. They tend to modify the exposure on their own and in many cases without complex lighting the exposure they suggest is pretty acceptable. I was educated using center weighted and spot metering and I use spot metering often. These modalities of exposure meters give us an exposure which is very accurate for a subject of middle tonality (Middle Gray) but they fail miserably to give a correct exposure when the subject is very bright or very dark. The skilled photographer knows what to do under those conditions for the correct exposure adding more exposure for the bright subject and less for the dark one.

Today a large proportion of photographers use Aperture Priority as their main shooting mode. It is very convenient because we select the aperture we need for depth of field and the camera sets the appropriate shutter speed for that aperture. If too bright we set the base ISO of the camera and if too dark we raise the ISO setting for a better response to low light levels. Most modern cameras do pretty well up to ISO 1600 from there on some cameras are better than others and in addition there are excellent softwares to control noise. Problematic subjects require exposure compensation.

I hope with these simple comments I have not drifted too far from your topic. Keep practicing what you have learned and keep in mind that shutter speeds and apertures are used creatively. We use apertures to control depth of field and shutter speeds to control motion. Many books on exposure will explain this to perfection. You will find lots of information in the Internet about exposure and using the Manual Mode but I want to repeat it again, practicing makes perfect and if you have a local camera club or someone with enough experience you can learn even more and faster.

Good luck.