Use AF when you can. Use manual when it is advantageous to.
There are several fairly common situations where AF won't work very well.
In the D7000 user's manual (page 93) Nikon describes those situations.
Canon user manuals have a similar section in them somewhere.
Since AF is not a be all to end all when it comes to focusing the lens we really should be skilled at doing both manual focus and auto focus.
Nikon AF mods can be release priority or focus priority.
By default AF-S (single focus) is focus priority
By default AF-C (continuous focus) is release priority but can be changed to focus priority in the Custom Settings menu - a1.
If you are using a manual focus lens, or an AF lens in manual focus mode, the D7000 has the Electronic Rangefinder manual focusing aid that will light the in-focus indicator in the viewfinder when focus has been manually achieved. See page 100 of the D7000 user manual.
And it may be useful to review pages the entire
Focus section of the manual that starts on page 91.
An additional key part of focus is knowing how to control depth-of-field (DoF) to your advantage.
Several factors determine how deep or how shallow DoF is.
Point of focus (PoF) distance has a big effect. The closer you are the shorter the PoF and the shallower the DoF.
Wide lens apertures contribute to a shallow DoF
IF the closer the PoF is to the camera. In other words if the PoF is far from the camera the DoF contribution of a wide lens aperture as far a shallow DoF is concerned diminishes.
A common misconception is that longer focal lengths deliver shallower DoF. Longer focal lengths require increasing the PoF distance to maintain subject scale in the frame. With subject scale the same in the frame, longer focal lengths deliver the same DoF at the same lens aperture as the shorter focal length lens.
What does change is the field of view (FoV) and how much background elements are magnified (background compression) using a longer focal length. As lens focal length increases FoV gets narrower and back ground elements are larger (magnified). If the magnified background elements are blurred by a shallow DoF many interpret that as shallower DoF, but it is the background compression
Understanding Camera Autofocus
Understanding Depth of Field in Photography
Tutorials - Sharpness