How did Phillip and Timothy survive the hurricane in The Cay?

Phillip and Timothy survive the hurricane because of solid preparation and a lot of luck. Their preparations begin in chapter 14 when they realize that a big storm is quickly approaching. Phillip ties the keg to a palm tree, and he ties the rest of the rope around a palm for them to cling to if the storm surge gets too high. They also eat a large meal because the fish will not return to the cay for several days after the storm if finished. When the storm does finally hit in chapter 15, Timothy and Phillip take shelter in the hut. The hut eventually breaks apart in the storm, and the two characters retreat to the palm tree and tie themselves to it. Timothy positions himself so that his body takes the full force of the storm, and his body serves as a shield for Phillip. The storm rages on, and both of them survive the storm; however, the storm has battered Timothy so badly that he dies soon after. Phillip is now "blind and alone on a forgotten cay."

How did Timothy protect Phillip from the storm in The Cay?

In Chapter 15, a large storm washes over the island. The wind blows over the hut in which Phillip and Timothy live, and Timothy protects Phillip by covering Phillip's body with his own. They spend two hours that way, as the storm blows over them with lashing rains and strong winds. The storm is so harsh that they can barely breathe.

As the sea begins to come up the beach, Timothy brings Phillip to the palm trees on the rise for shelter. Timothy ties Phillip and himself to the tree. Water laps against their ankles and feet, and Timothy continues to protect Phillip with his body against the driving wind. They remain that way for about an hour, until the wind dies down and they can untie themselves from the tree. When the eye of the storm passes over and the winds pick up again, worse than ever, Timothy again ties Phillip to the tree and protects the boy with his body. Several large waves pass over them, and, in the end, the storm kills Timothy while Phillip survives. Timothy gives his life to protect Phillip. 

How did Timothy and Phillip position themselves against the tree during the hurricane in The Cay?

Unfortunately I had to edit your original question because it contained multiple questions, which is not permitted under eNotes regulations. Please make sure that in future you restrict yourself to asking one question at a time.

You are refering to the incident when the hurricane strikes the island on which Timothy and Phillip are residing which occurs in Chapter Fifteen of this novel. The hurricane is of course incredibly strong, and quickly blows away the hut that they made, so Timothy takes Philip to a tree for protection. Note the way that they position themselves:

Standing with his back to the storm, Timothy put my arms through the loops of rope, and then roped himself, behind me, to the tree.

We can see here another sign of how Timothy cares for and looks after Phillip. In spite of the tensions in their relationship because of Phillip's racism and the way that he has been brought up, he willingly chooses to use himself--his own body--as a barrier to protect Phillip from the rage of the storm, giving Phillip the protected space behind the tree trunk.