The whole thing to keep in mind is that the passion and the structure of stories work in tandem, but not as partners. Like our own reason and emotion, sometimes they agree, sometimes they are at war, but mostly they hold to an uneasy truce built on a compromise that is unsatisfying to reason and unfulfilling to emotion.
Because they are not the same, reason and emotion can never fully line up. When they match in one place they must, by their very natures, differ somewhere else.
The real key is to become wise in the ways of giving each its due and knowing where to do it. Where is it more important that things make sense? Where is it more important to let feelings run like the wind?
If you would like a general rule of thumb that will get you most of the way there, it is this: Let reason rule the plot and passion rule the characters. You plot is the most logical part of your story and your characters the most human. So let you plot always make sense and your character always ring true.