a. Which shaded area are you referring? In Meteogram the explanation is given in posts here above.
b. Check High, Medium and Low clouds layers. If necessary see More layers... The direction of the sun is given by a plugin only available on website. Menu > Install plugins > Sun position
c. You probably mean in case of temperature inversion, which brings a cloud / fog layer below the inversion. You can check that by using the Sounding feature. Right click on mouse.
Note that the weather model can only show this phenomenon at large scale but not in local conditions like in a mountain valley.