For anyone wanting to learn this more in detail I highly recommend the book "Understanding Exposure" by: Bryan Peterson.
My personal approach to taking handheld photos in manual mode using natural light is as follows:
1. Look at the scene and determine what the most important factor is. For example: * Do I need to freeze motion? Then I need to set a short shutter speed. * Is the image being taken in low light? Then I probably want to open the aperture and set my shutter speed as long as is suitable for what I can hold. * Do I need a large depth of field or to maximize sharpness? Then I need to set the aperture to a suitable value to achieve that.
2. After I consider the most important factor and set either shutter speed or aperture to a starting value, set the second most important factor using the same thought process.
3. Adjust the ISO so the image is exposed properly. Knowing your camera, is the ISO going to result in an acceptable image? If not, then go back to the first step and adjust your shutter speed and aperture to bring the ISO down to an acceptable value.
4. Take the photo and review.
Of course, this doesn't apply to every scenario but it generally is a good approach for the types of photos where the exposure settings are critical. If I'm shooting a landscape outdoors, then I'm probably starting off by setting ISO to 100 first and then the aperture to the sharpest value for the particular lens I'm using as I'm sure that the shutter speed will be acceptable regardless of what it ends up having to be or will be what drives me to use a smaller aperture.