There was a good thread two years ago.

Copy/pasting my answer (check the thread, there are more comprehensive ones):

At the time of the Crusades, they probably knew about the differences and enmities.

During the siege of Antioch, a delegation was sent by the Fatimids (Shia - base of power in Egypt) to the crusaders to propose an alliance against the Seljukids (Sunni - base of power in modern Iran, Iraq and Syria at the time).

Guillaume de Tyr writes (rough translation, I read it in French) "For very long, there had been a grave hostility between the Easterners and the Egyptians: this ingrained hatred stemmed from the difference of their superstitions and their contradictory dogmas."

Albert d'Aix writes about the meeting and indicates that Fatimids and Turks are foes but without theological precisions. Raymond d'Aguilers only mentions the embassy.

Sources :

• William of Tyre, A History of Deeds Done Beyond the Sea
• Albert of Aachen, Historia Ierosolimitana
• Raymond d'Aguilers, Historia Francorum qui ceperunt Iherusalem