I usually advance with a main body of crack troops to attack and destroy settlements. I enslave it to the max using the multi-enslavement tactics. So the resulting settlements gets reduced to 1500-2000 pop.

If you dont like using this then, another way is to have a full stack of peasants following ur main troops around and securing the cities u have acquired.

If u use Seluc, make sure to bring Onagers to attack the settlements, as the phalanxes are next to useless fighting in the city walls. If u have SS Legionary, then its another matter. But come on, its hard to retain these bad boys. Better to just destroy the walls and let the phalanxes through. They are awesome in city fighting, if u make sure they dont drift to the right too much lol.