Hehe, I'm a student of cognitive sciences so I just have to reply.
Yes, the claim that we only use a fraction of our brain is a popular misconception, we use pretty much all of our brain but our equipment for mapping brain activity has been very limited but with enhanced fMRI it has become a lot easier.
The traditional perspective on cognition has been to consider the brain as a closed system with input and output, the strictest form of this approach was the Behaviorist theories. However, beginning 1957 and the publication of Noam Chomsky's, among others' research, challenged this point of view. Ever since the cognition has started to be seen in context rather than isolated.
Today "situated cognition" is what is by many considered an accurate approach to the problem. "Situated cognition" doesn't just aim to explain the workings of our minds but also how we interact with out environment and how we use artifacts (man-made items) to record and move cognition from our minds to the environment we interact with and in that manner allows us to share our mind spaces with other people. An Internet bulletin board system such as this is a perfect example, it could not exist without our interaction with our environment. Out success as a species is most likely directly related to our physical bodies. Dolphins might be smarter than us, for all we know, but they can't store or exchange information nearly as well as we can.
Cognition takes place in the world, not just in your brain and that is something you need to keep in midn when you try to model thought.
Then, there's reason and emotion, or not? Are emotions and thoughts strictly different, is logic void of feeling? Should logic be void of feeling? But that's a wholly different discourse.