Deciding when to use manual focus and when to use auto focus can be rather confusing. When you use auto focus, the camera decides what to emphasize in the picture. You can readjust the auto focus by holding down the shutter button, but other than that, you have very little control. For more serious photographs, most professionals use manual focus. Manual focus provides them with more control and the ability to set up the shot the way they want it.
If you do decide to use manual focus, you have complete control. You decide where to set your focus. Manual focus, however, is much more labor intensive.