I am writing an essay on the 'goodness' of both Finny &Gene?I have found several situations where one or both are good.My problem is that in...

Concerning the essay you're writing about A Separate Peace, I suggest you alter your thought and thesis slightly. 

First, well-developed characters in good fiction are usually mixtures of positive and negative personality traits, or good and bad, as you say.  You seem to want to show that both are just good, since you mention wanting to ignore the character that doesn't show goodness in a particular scene.  That's probably a mistake.  A literary character doesn't have to be completely good.  It doesn't take anything away from the character to show the negative.  That makes a character more realistic.

Furthermore, just because both characters have goodness in them, doesn't mean they have to show it in the same scene.  Can't you just show goodness in Gene is a few scenes, and goodness in Finny in a few different scenes?

I guess what I'm suggesting is that you really don't have a problem.  Just make sure your thesis doesn't try to argue that either character is completely or totally good.