I say you have Governors and Generals, only one per city (or army). Traits and Abilities can alter your effectiveness as Either, and Acadamies (menioned in earlier posts) can increase your Administrative traits and your Commanding traits.
some Governors give a malus to tax collection but a bonus to farming and mining income. some Governors might have high bonuses in taxes and trade, but penalties to happiness/morale.
In ROME there were some traits which made you more popular with the people/troops, and other traits that made you more popular with the Senate/Nobility. Sometimes becoming more popular with one group made you less popular with the other.
anyways, it was usually better for a city to have a family member to over-see the City if they had at least 1 in administration(management) stat.
I think the Architecture/Prestige School of thought, Combined with the Education school of thought, could lead to the building of these "Acadamies" which will allow your family members/statesmen to learn how to manage cities more properly (although some can naturally gain these traits with a good bit of luck).