In Lord of the Flies, Chapters 1-3 , how do the boys set up the island as civilization?

The boys establish a model of civilization by first creating a hierarchy and, later, by organizing groups of boys who are assigned various duties.

The fact that Ralph's father is an officer in the military suggests that the boy's home life has most likely been structured. When Ralph takes the shell from Piggy and water runs from it, Ralph notices a hole. He then inspects the shell. It dawns on Piggy that Ralph is thinking of using this conch. When Ralph says, "we can use this to call the others. Have a meeting. They'll come when they hear us" Piggy brightens. Piggy then asks, "That's why you got the conch out of the water?" (Ch.1). Ralph's only response is to have Piggy explain how his friend blew his conch. 

After Jack Merridew and the boys of the choir respond to the call of the conch, Ralph recognizes Jack as having "the voice of one who knew his own mind." Jack, in fact, starts to take the lead by saying, "We've got to decide about being rescued"(Ch.1). Ralph suggests that there should be a chief to decide things. This suggestion prompts Jack to suggest that he be chief because he is already the head boy of the choir. When "the dark boy," Roger, speaks up and calls for a vote, the boys raise their hands for the leader they want. The majority chooses Ralph because of his appealing appearance and because he holds the conch. Only the boys in the choir have voted for Jack, and their votes have been cast out of "dreary obedience."

Later, areas are designated as latrines, places are marked for where shelters can be made, and an elevated area is established for the very important signal fire. The boys survey the island to learn what is available to eat and what can be used. Ralph points to "a platform of forest" and remarks, "down there we could get as much wood as we want." Not to be outdone in leadership, Jack later insists, "we'll have rules! . . . Lots of rules! Then when anyone breaks 'em." He wants rules so that he can punish any who break them. On the other hand, Ralph tries to reassure the boys that there are no beasts and that all the islands have been discovered. His father, who is in the Navy, has told him that there is a map belonging to the Queen on which every island is named.

Piggy is the counselor, the voice of reason. When the boys start the first signal fire, it gets out of control. After seeing the devastation caused by the wildire, the boys fall silent; Piggy scolds them, telling them that they must "put first things first and act proper." They must not run off without working on the shelters, they must be careful about setting fires, and they must give Ralph time to think. However, when Ralph asks for the list of names of all the boys on the island, Piggy tells him that he has not had the time to compile it. Nevertheless, they realize a boy who had a birthmark on his face is missing.

With the discovery of pigs on the island, Jack designates himself and his choir as the "hunters," who are now exempt from working on the shelters. Ralph then tries to explain to Jack the importance of the shelters, which includes not just protection from the rain, but a safe place for the boys to hide from their fears of the unknown. Simon intervenes because he intuitively understands that superstition needs to be countered by civilization.