Gary is spot on - if the AF point isn't where you want it, then it's completely premature to question the AF system or start wondering about DOF. You have to get the focus point right before anything else even has a chance of falling into place.
Start with the basics - set your AF system to single point, and when shooting, use the 4-way selector to choose where you want that point. I recommend setting your camera to focus from the AE-L/AF-L button and leave it in AF-C, but assuming you focus using the shutter release, for portraits, set the camera so AF-S, and for moving objects, AF-C. press halfway and give a second for focus (and VR) to settle. Elbows braced against your body, breathe slowly, and gently squeeze (don't press or stab) during your exhale.