well im totally confused as to what the problem is :-\
99% of the time you will not need manual focus especially on an 18-55mm lens. There is not need to select manual focus on the camera as it will change with the lens switch, on camera try selecting AF-C this is continuous auto focus and will refocus constantly while you have the shutter release half depressed.
when looking through the viewfinder you will see the black dots light up red to indicate that those points are in focus. not all will light up at the same time unless photographing something like a flat wall.
if you are selecting manual mode on the camera dial then you really need to make sure you know what you are doing with the camera before you start as the settings wont be right and it may be set to a slow shutter speed resulting in blurry photo's, also manual mode may have the camera set to manual focus even if the lens is not so check on the screen the right hand side says "AF-A/AF-C/AF-S" hope this helps as this is my interpretation of the question.
if you post some of these pictures on the forum we should be able to see the settings you used and may be more help.
failing that i would go to the camera shop where you bought it and ask them to help you as things are easily solved in person