This novel is set in 1942 at Devon School, the fictitious name for Exeter Academy, the all-boys boarding school that author John Knowles attended. Phineas is modeled after Knowles' college classmate, David Hackett, and Brinker Hadley was inspired by Gore Vidal, a gifted writer who also graduated from Exeter Academy. The novel is the story of Gene and Phineas and their evolving relationship over the course of their senior year in high school..
Note that the novel is set against the background of World War II. This serves as a foundation for the "war" that exists within Gene Forrester throughout the novel. This book is filled with motifs and symbolism, namely -- the tree, the marble stairs, water, Eden motif, songs motif, and the significance of the title.
The link to the left gives some concrete knowledge and evidence of what you are reading.