I am listening to an historical fiction audiobook and a character said the phrase "use your brains" to insist that his men acted smartly. Would someone from the 1000-1200 time period know that the organ within the head was used to act intelligently?
Even just using one example of literature from 12th Century Byzantium, Anna Komnene's famous Alexiad, we find phrasing linking the brain with intelligence used at least three times. Because Anna writes these simple phrases without any detailed explanation as to their meaning (which she does in cases of obscure references to mythology or science), it is natural to assume that the relationship was commonly understood amongst those who would have read her work. I have reproduced the relevant examples below for you to read.
Book III: The Accession of Alexios
"Therefore in all daily business he did nothing, not even a trifling thing, without her advice, but made her the recipient and coadjutor of his plans, and gradually he stole a march upon her and made her a partner in the administration of affairs, sometimes too he would say openly that without her brain and judgment the Empire would go to pieces."
Book X: The Wars with the Cumans and the First Crusade
"After a short rest from his many toils, he found that the Turks were overrunning the interior of Bithynia and plundering everything, and that on the other side affairs in the West were calling for the Emperor's attention. He was more troubled about the former than the latter (for his business was naturally to attend to what was urgent) and he devised a device which was really magnificent and worthy of his brain, and by this contrivance he safely fenced off Bithynia with a canal against the Turks' incursions."
Book XIII: Bohemond and the Treaty of Devol
"For the Emperor had not received any letter of the kind from the other side, either from Richard or anybody else, with suggestions of good-will and trust; but he alone out of his own brain conceived this species of letter."
In addition to these excerpts, there is also other evidence that supports a general understanding amongst the educated of the period regarding the functions of the brain, including an entry in the Byzantine Suda, a 10th Century encyclopedia, that reads:
"Thus, when the hollow at the back of the brain is injured, the faculty of memory suffers, and if the brain is injured otherwise the rational faculty itself suffers"