On [this map] (http://upload.wikimedia.org/wikipedia/commons/a/a0/HRR_1400.png), of the Holy Roman Empire in 1400, many of the small, independent states are geographically divided. Also, the Kingdom of Sweden owned parts of the German coast in the 17th century if I recall correctly. How was it possible to govern these areas?
That's what governors are for. Under many European royal systems a governor would be given a commission and vested with certain executive authority. So the monarch picks whoever they think is most capable and delegates authority to him.