For half an hour the glass-bottomed boat drifted. pitching and rolling above the
reef in four- to six-foot waves.
a. fragment
b. run-on
c. correct

There are actually two sentences here.  Because it is not indicated to which sentence you are referring, I will look at both.  

For half an hour the glass-bottom boat drifted.   CORRECT

Pitching and rolling above the reef in four- to six-foot waves.  FRAGMENT

The second sentence is a fragment because there is no subject within the sentence.  Even though it can be determined that what is being pitching and rolling is the boat, sentences should always be considered independently of each other.  Thus, when look at the second sentence we are not told what is doing the action.  As such, it is a fragment.  

1. list two reasons why fossil fuels should continue to be used as a source of energy in america.

specific audience will understand the main ideas. for example, if you were writing an instruction manual for rocket scientists, it would likely look very different from one you would write for young children. your language, tone, and writing style would change significantly.