One thing is how the brain works as per the functions we display (behavior, thought patterns, conditioning, etc) and another the way we feel and act based on clinical things such as neurochemistry, lesions in areas, etc. Completely different.
I was a behind-the-retina visual neuroscience guy for years, and we used to delineate the world exactly that way. We considered ourselves the "hard science" guys and the psychology/development/behavior guys the "soft science" guys (we had snide names for them, like the School of Arts and Crafts).
The older I get and the more I observe, the more I'm convinced that both sides are co-mingled in some really bizarre ways.
1) I do think that the hard-science aspects of your brain (neurotransmitter levels, overall brain state, synaptic organization, genetic variations) have a huge impact on how you react to the circumstances in front of you. Within that tiny, 2-10 second decision-making period, you're almost 100% on autopilot. Over the immediate time interval in front of you, you're in far less control than you think.
2) But I also believe that the soft sciences stuff gradually remodels the hard-science aspects of your brain over time. The mantra "fake it till you make it" is incredibly accurate. Behavioral overrides of existing patterns over a long enough period of time will undoubtedly lead to brain chemistry changes that make them more comfortable -- but that door swings both ways (it can make things worse as well).
3) And finally (as if anyone cared, fuck you guys in advance), I think we like to think that our frontal lobes assess situations and guide us toward action. I personally think that a huge majority of the time, our older brains make the call and our frontal lobes actually spend their energy justifying the decision.
tl;dr