what is the seperate peace within this novel

I am not sure exactly what you mean, but Finny and Gene have a kind of peace when they are best friends, but Gene never achieves that feeling of peace again after he shakes the branch and injures Finny. They achieve a kind of peace when the "trial" happens, but their "peace" is something they must face individually: Finny has to achknowledge that Gene hurt him in order to achieve peace, and Gene has to face the horror of what he did to his best friend in order to achieve some kind of peace.