How do Phineas and Gene grow throughout the novel?

Gene and Finny are roommates in A Separate
Peace, and your question asks how they grow.  Growth implies moving forward,
and I'm not so sure either of them makes forward progress in this novel; however, they
do each undergo a dramatic change.  Phineas, once an eternal optimist and idealist who
saw the war (and, frankly, everything else) as some kind of a cosmic game, is
transformed into a bitter realist.  He still claims the war is a giant fabrication
created by old men, but he doesn't really believe it anymore.  The change, of course, is
precipitated by the reality of Gene's disloyalty and (though he doesn't want to admit
it) momentary hatred.

Gene is more of a realist, committed
to achieving and producing, though he loves neither.  He is a friend to Finny, though
Finny is a better friend than Gene.  Gene gets frustrated at Finny for all the
distractions and the dares (jumping from the tree) and the  devilish antics which keep
Gene from moving forward on his plan of achievement.  Somehow Gene determines that Finny
is deliberately trying to sabotage him for his own gain; it's not true, but in a moment
of anger he jounced the limb which ultimately leads to Finny's death.  Nearly the moment
that happens, Gene realizes his mistake, but it's too late.  His outward change, then,
is from friend to enemy and back to friend, though damaged and broken.  Internally, Gene
goes from believer to cynic, back to believer then back to cynic.  There are lots of
ways to phrase that journey, but that's essentially it.  Gene is a more complicated
character, of course, because we meet him many years after the event, as well.  As an
adult, he can be read as having changed and grown from his experiences at Devon; or he
can be seen as having undergone no change at all, still cynical and still rather
angry. 

If loss of innocence is growth, these two
characters grow---a lot.