The bakufu didn't interfere with the Imperial Court in Kyoto or with the shoen and public territories in rural areas, instead creating a dual system of government (bakufu and Court) under which it had the power to appoint warriors (as opposed to Court noblemen) to the key positions, including the jito, that controlled the countryside.
京都の朝廷と地方の荘園・公領はそのままで、地方支配に地頭等の形で武士が割り込む二元的な支配構造ができあがった。