The Ecclesiarchy was not a creation of the Emperor, who -- despite his immortality, power and autocratic rule -- did not want to be seen or worshipped as a god. The Ecclesiarchy emerged three millenia after his incarceration in the Golden Throne out of various cults and faiths based around the Emperor, which gradually grew powerful. In the 41st Millenium, it is one of the most powerful institutions in the Imperium of Man.
Despite being the only official church in the Imperium of man, the Imperial Cult varies immensely, with a myriad of sects, mostly descended from earlier faiths, with worship of the Emperor added over time after conquest by the Imperium, as well as unusual philosophical positions. However, despite this internal variation, the Ecclesiarchy can be extremely dogmatic at times and willing to declare minor deviations among a population that would otherwise be ignored as local customs as Heresy, condemning millions to death.
Despite this, there are several groups which exist outside the Ecclesiarchy's control in the Imperium. Among these are the Space Marines, which have their own warrior cults that venerate the Emperor as the apex of humanity -- but not as their god, and the Adeptus Mechanicus, which are a largely separate element in Imperial society and have their own set of religious beleifs revolving around the Machine God (Omnissiah).
The head of the Ecclesiarchy is the Ecclesiarch, one of the High Lords of Terra.
The armed forces of the Ecclesiarchy are the militant wings of the Adepta Sororitas.