Emotions in Science?

I have an urge to take issue with this, but let me first ask what you might consider the appropriate 'tools' to be?Also, what do you mean by 'as they are meant to be understood' ?
What criteria might be used to determine that?I am going to be a little pre-emptive here and point out that, for purposes of effective discussion, we will need to separate our 'understanding' of emotion into proximate and ultimate causes.Proximal causes might comprise biochemical states, etc.
Ultimate causes can only be explained by evolutionary theory.
Emotions are manifestations of the phenotype that are not going to be immune to selective forces.

I think your breakdown is not far off the current consensus.Emotion seems linked to imagination and both are activities believed to be mediated by the cerebellum, the most derived part of the brain.Imagination, intellect and, at the most basic level, emotion, are all thought to reside there.