The brain is far from understood, if it were simple enough for us to understand then we would be too dumb to understand it. However, we do know a lot about it. Only quite recently the plasticity of the brain has become accepted - it used to be thought that the brain structures were fixed and that they filled up with knowledge and experience, much like a computer. I remember as a boy being taught that the number of neurons in the brain grew until adulthood and then they just started dying off with no new ones replacing them. The truth is more complicated - our brains form new connections all the time and can become rewired dramatically through necessity if one area becomes damaged, but generally there are structures in the brain that perform [more-or-less] specific functions.
People sometimes talk about being left or right brained, i.e. more dominant in the left / right hemisphere.
The left hemisphere contains the structures strongly associated with: grammar and vocabulary; logically structured thinking; analysing and controlling feelings; reality.
The right hemisphere contains the structures strongly associated with: intonation of speech; an unstructured approach to tasks (they call it 'multitasking' which has been shown to be less efficient in tests); emotional responses; fantasy.
To summarise, the left brain is rational, and the right brain is a hippy.
No prizes which side I'd be associated with, although actually I'd say I am much better than average at seeing the big picture - the less immediate consequences of actions - which is a right-brain trait.
The 2 hemispheres communicate by little roads called commissures, and one superhighway called the corpus callosum.
For severe epilepsy this superhighway of communication is sometimes severed, leading to some fascinating discoveries. The two halves of the brain can be thought of as having separate consciousnesses! Imagine being trapped inside someone else's head, much like in the film 'Being John Malkovic', able to see everything but only able to have a slight influence on his behaviour. That may be happening inside you right now! With some subjects who have had their corpus callosum severed, a written command can be flashed up visible only to the eye without the subject being consciously aware of it. For example, if the word "LEAVE" is flashed up, the subject may get up and start to leave the room - when asked why they are leaving they reply something like "I'm thirsty, I want to go get a soda". The right brain has invented a story for the the conscious mind that is coherent with the action demanded by the subconscious.
Some of these patients also experience 'alien hand syndrome' in which one arm is under the control of the 2nd hidden consciousness. Freaky.
I wonder if the religious doctors see these patients as having 2 souls?
Most people invent stories for their lives that fit with their actions. Most people believe they have rational reasons for their actions, but actually it is just lies told to them by the ultimate manipulating puppet master - their own subconscious.