My take is that the old brain structures are configured to work somewhat like a Hopfield or Boltzmann network with each of the nodes being one of the basic behavior states like feeding, fleeing, fighting, mating, seeking shelter, sleeping, drinking, exploring, grooming, nesting, whatever else you can think of.
The various body sensors are inputs to this tipping the current state to whatever has the strongest input.
The sensory system has memory associated with it that registers the elements of the environment with straight Hebbian learning that takes some time to consolidate.
The memory system can have the learning rate modulated by various sensations such as “reward” or “punishment” which both increases the learning rate and has specific memory receptors to color the stored sensations as good or bad.
Future recognition of the same sensation keys into both recall of the specific sensation and the paired good/bad weighting.
A simple example that most people are very familiar with - you eat something and shortly after you eat it you forget all about it after a short while. It turns out that it makes you violently ill and you vomit. After that event seeing or smelling that food may make you queasy and you have absolutely no desire to eat it. It’s as if the last thing you ate was held in a buffer somewhere and when you experienced pain from the last meal the learning rate and negative association was boosted in the memory consolidation.
This is mostly below the level of the cortex but the amygdala does exert an influence in modulating the learning rate in the prefrontal cortex and coloring the judgement of experience as good or bad.
This adds weight to various learned motor programs and influences the section of the appropriate program for the situation at hand.
In the Rita Carter book “Mapping the mind” chapter four starts out with Elliot, a man that was unable to feel emotion due to the corresponding emotional response areas being inactivated due to a tumor removal. Without this emotional coloring he was unable to judge anything as good or bad and was unable to select the actions appropriate to the situation. He was otherwise of normal intelligence. [1]
This evaluation and flavoring of your perception is done by subcortical structures below the level of consciousness.