Question: what was generally the preferred way for european powers to control colonial regions?
Answer: Indirect rule

Indirect rule is a system of government used by the British and French to control parts of their colonial empires, particularly in Africa and Asia, through pre-existing local power structures.  These dependencies were often called "protectorates" or "trucial states". By this system, the day-to-day government and administration of areas both small and large was left in the hands of traditional rulers, who gained prestige and the stability and protection afforded by the Pax Britannica, at the cost of losing control of their external affairs, and often of taxation, communications, and other matters, usually with a small number of European "advisors"