The second dream, with its heavenly bodies, foretold the spiritual attainments of Yosef's which would ultimately be recognized by his entire family. These achievements became a part of his very being and their bowing was to Yosef himself. We tend to think of three ways to spend our time - constructively, destructively and doing nothing at all. Our Sages teach that HaShem created our drive to do evil as well as our drive to do good. But He gave us the Torah as the means to battle our evil desires.
Water is a symbol of the Torah.
Obviously if the pit is empty, no water is in it. The Torah hints to the lesson that a lack of water, Torah, produces a vacuum that pulls in dangerous creatures, evil desires which can only be controlled by learning Torah whenever possible. Reuven could go anywhere with his brothers because they were all equally guilty. However he was afraid of his particular responsibility for Yosef's fate. The fear that had driven the brothers to commit the crime was the fear that their independence would be overpowered by Yosef.