Silvio - Kudos for sharing your profile, in which you say your main photography effort is portraits. That makes it easier to propose an answer to your question about manual focusing.
There is really no way to get an entire image in focus unless all of the subject is in a single, very flat plane. There will be a point of focus and then -- varying by depth of field -- areas of acceptable sharpness and areas more out of focus. These are optical facts of life that cannot be gotten around without tilt lenses and backs -- and then you are shifting your plane of focus, a'la view camera, so that's not a good comparison for a DSLR's capabilities.
I am a former Navy photojournalist who was trained at Syracuse University in 1972-73. I was blessed to have a former Navy journalist by the name of Bob Moser as one of my teachers. Bob was draconian in demanding crisp focus. For people pictures, he drove home that we don't just focus on the face, nor the eyes. The point on which we need to focus is the nearest eye, and on the pupil at that! He taught that of the pupil of the nearest eye is in focus, the rest of the image is immaterial -- the image will appear to be in focus. If instead, it is the far eye, or the nose, or ear that is in sharp focus, the picture will register to the viewer as fuzzy. Look at great portraits and you will see this if you seek it out.
As Alan Olander indicated, using a single point of focus and manually adjusting the focus until the red focus light is on, is a good way to do this with a DSLR. Sadly, unless you buy an after market split image focus screen, and I am not sure they are available for all Nikon DSLRs, that's the best way to achieve focus.