Q1: Only the first input is used. It doesn’t matter what you put in the second input.
Q2: Thats a bit trickier because in a Shader/Material you have only access to the data from the current object. In your case the earth. To get position and rotation values of another object in your material you need to use drivers. Just use 3 value nodes (x, y and z) and create a driver for every input that is driven by the x, y and z position of your sun lamp. Here is a good tutorial for using drivers: https://www.youtube.com/watch?v=BJJJpWcxp0o
Q3: Here is a basic lightning tutorial: https://www.youtube.com/watch?v=gTMORaEygRE. If you have any concrete problems with lightning you could share the *.blend file with the earth.
Q5: Not sure what you mean. Yes, you can animate / keyframe node inputs. Just set a value, got to the desired keyframe, hover your mouse over the value and hit “I” this will (I)nsert a keyframe.
But I would create a second sphere for the clouds. This is more realistic and should look better. Than you dont have the problem with faking shadows, because Cycles will create realistic shaders based on your lightning. And one sphere more isn’t that much more geometry.
If you want a really realistic atmosphere, have a look at this great atmosphere shader. It will take for ever to render but it looks so nice.