Should one focus Manually or let the camera do the auto focusing ? This question is most often asked. As long as the end result is achieved, that is a perfectly focused photograph, it does not matter, if you focused manually or on auto focus mode.
Also remember, the focusing mode you choose is not linked with the shooting mode you choose. If you are shooting on manual mode it does not mean that you need to focus manually also. I have come across a lot of people who focus manually just because they have been shooting on the manual mode.Your shooting mode is related to exposure and this could be totally manual or programmed.
However, also keep in mind that the Evaluative / matrix metering of your camera is influenced by the focusing point your choose manually or on autofocus. Switching to autofocus does not mean that you do not have to do anything manually. You still have to overlap the focusing point on your subject and if you have multiple focusing points, shift the focusing points to overlap your subject. In one of the modes, it will automatically focus on the element nearest to the camera and well, you need not do anything except ensure that your subject is the nearest thing in the frame !