Thoughts about the brain

Neuroscience has discovered that what makes our personality and behavior is dependant on an inner chemical laboratory:
serotonin for harm avoidance, dopamine as regulator for novelty seeking, norepinephrine controlling our reward dependance, oxytocin as social contact regulator, endorphin managing pleasure...
That makes human thought dependant on stimuli ( electrical) or chemistry. In other words we are much less free than we think. If I can make you feel sad enough to almost commit suicide by stimulating a specific part of your brain, where does your own self come in? Or to spin the thought further- if all of our thoughts are electricity and chemicals what are we without our body?
On the other hand if the chemicals control the way we feel and think, there is also a way to control the chemicals. You can calm down in taking a deep breath ( and lower your adrenaline high) - what brought you to the decision to calm down?- there was a choice: you could have become more excited! Was there more or less serotonin involved in making a choice? Or to spin this thought further: is there first an impulse thought - or is there first a chemical? ( the old hen and egg question)
On more complex levels- thought can make you sick - or it can cure you or help in the cure- which means that the mental chemistry and the chemistry of the rest of the body are closely linked. Who has the final power over whom?
All the neuroscientifical research explains about conscious behavior and its deviation reasons- what about our subconscious? Since we don't really know what is in there how can we know by what it is controlled?
And where does patterning come in? Our bodies and minds are constructed not on detailed static chains for actions but on patterns that can be adapted to contents of situations. Patterns are repeated from the simple to the complex. ( ex. the learning mechanism of a child uses the pattern of 'copying' of cell- growth) Are the chemicals the 'patterns' of our brain?
What is the role of hazard in this chemical laboratory? Is hazard our freedom of choice chemically speaking? ( a molecule was walking by by accident and fitted into the receptor?)