Great question! It is true that the beginning of the prologue uses the tower and the dungeon as representations of Heaven and Hell. On an even deeper level, the tower represents God's Truth and the dungeon is filled with prisoners who represent the damned souls that occupy Hell. The prologue further expounds upon the ways in which Will's dream are connected to his quest for morality and justification.
The world between the tower and the dungeon represents mortal life, which determines where all living souls will end up. Will is urged by a woman who goes by the name of Holy Church to obtain the Truth found in the tower, but he faces many obstacles in pursuit of this moral goal. Holy Church warns him that his soul's salvation rests on following Truth and that the dungeon is full of all Wrong in the world. The dungeon is also associated in the text with Satan. After this initial warning, Will witnesses a marriage arrangement between Lady Mede, who represents Reward, and False. This setup is a representation of the false reward that comes with choosing Wrong. Instead, the king of London suggests that Lady Mede should marry Conscience. This sparks a moral debate on whether Reward is a matter of falsehood or good conscience.
Lady Mede is the primary source of conflict between Theology and Holy Church as well, and this conflict is the catalyst for Will's journey. Later in the text, the moral themes presented in the prologue gain more depth. As Will receives a second vision or dream, he preaches to others in an effort to compel them to repent of their sins. On another level, the prologue explores the nature of morality as it relates to the different social classes. In the beginning of Will's vision, he sees beggars, noblemen, clergy, and workers all engaged in their normal duties. While their lives are different, the moral conflicts they face all lead to the same eternal consequences. All major aspects of Will's visions are connected to morality in similar ways. The different people he meets represent either aspects of humankind (the king of London, for example) or a moral dilemma (the marriage conundrum between Lady Mede, Conscience and False.)