The title from John Knowles' A Separate Peace "is taken from Ernest Hemingway's novel A Farewell to Arms, in which the book's protagonist, Lt. Frederic Henry, declares his own private armistice during World War I" (from, A Separate Peace Themes, here on enotes). I suggest that the title refers to the separate peace that each character in the novel tries to achieve and maintain. Each character has his own method, some more effective than others, though none is infallible. Gene says as much on the final page of the novel:
Other people [all but Finny] experienced this fearful shock somewhere, this sighting of the enemy, and so began an obsessive labor of defense, began to parry the menace they saw facing them by developing a particular frame of mind.
Quackenbush has his method, Leper has his, Brinker his, Finny and Gene theirs. Today we would associate this with "defense mechanisms." This, too, is a war story. A war story about adolescents trying to maintain a separate peace not only amid the usual teenage angst and everything that causes it, but also against the haunting backdrop of a war.
I think "A Separate Peace" refers to childhood, specifically the teenager years. If you take a good look at the circumstances of the novel, Gene does indeed have the major internal conflict of all the characters. However, you need to look at the opposite of peace to help define what it is: war. Age 18 means eligibility for the war and all these boys anticipate it as if it will determine the direction of their life... when they arrive at that senior year.
Prior to their senior year, and even a little bit during this senior year, the boys find ways to remain children or teenagers: blitzball, snowball fights, and drinking hard cider.
I also think this is a symbolic peace. We enjoy as children the least responsibility our lives will hold until age 18. After that point, our life is a war of struggling to pay bills, maintain relationships, and maintain a positive work life.
A "separate peace" refers to the peace that Gene must make within himself. It's not about a peace that's reached after a war, but the real struggle that is within the hearts of the characters. In his last encounter with Finny, Gene gets some peace of mind by understanding Finny's nonviolent nature. It isn't until he's older, after he's matured and understands the meaning of his relationship with Finny, that Gene can finally achieve total peace within himself and accept Finny's death without guilt. He understands the duality of man's nature, the good and the evil parts of man. He realizes fear and evil caused him to behave the way he did, and he's able to finally forgive himself because he sees that war took away his innocence, leaving him full of hate. He understands now that "wars were made instead by something ignorant in the human heart."