There are times I prefer to manually focus, but it's not necessary when setting a small aperture using the viewfinder. The camera will automatically focus using the largest aperture available on the lens and automatically stop down to whatever smaller aperture you select just before the shutter opens. After the shutter closes the aperture returns to full open. Even a lens with a minimum f/5.6 will focus with all your focus points, unless you use a teleconverter or nd/polar filters.
I have not tested how small an aperture is possible to auto focus using live view (it uses a different focusing method) and switching to the aperture ring for control.