In TEM focusing process, the objective potentiometers adjust the current of the objective lens in graded steps which must be used in succession. Course focus is normally done on the large phosphor viewing screen, while fine steps uses the binocular microscope on the small viewing screen.
Some objects are conveniently used to focus:
i) Membrane bilayers cut at right angle to their plane,
ii) Grain in the specimens,
iii) Fresnel fringes.
A tip is that focusing the image is often easier at low magnifications than at higher magnifications.
Based on the optical reciprocity theorem , BF-STEM images can be related to the HRTEM images of an atom as a phase object. Like HRTEM images, BF-STEM images are very sensitive to the focal conditions, and contrast reversal is often observed because of multiple scattering and phase shift due to defocus condition of the lens. A full interpretation of BF-STEM images can be done with phase contrast simulation in the same way as the HRTEM images. 
 Born M, Wolf E. Principles of optics. Cambridge, UK: Cambridge University Press; 1997.
 Spence JCH. High resolution electron microscopy. 3rd ed. Oxford: Clarendon Press; 2003.