Correct Aperture and Shutter Speed Combinations

Setting my camera to the right aperture and shutter speed combination manually is something that really puzzles me.  I know for example which aperture I would like to use to create a certain effect, for example to let a flower stand out from a blurred background, I would use a setting of f5.6 of f6.3 like in the picture below shot at f6.3:

What puzzles me is that if I had to set the shutter speed manually I wouldn't know what speed to select to get the correct exposure.  So I tend to let the camera select the shutter speed automatically.  It saves time and frustration that way, but ideally I would like to know how to do it manually.  I came across this very interesting article which clarified at least some of what I wanted to know:  http://photo.net/learn/basic-photo-tips/correct-exposure/

The exercise mentioned at the bottom of the article is definitely something worth doing regularly in order to get to know the correct aperture to use with which shutter speed under whichever conditions.  The article definitely explained a lot to me which I couldn't quite understand previously.