I had to same concern in my Roman campaign. While there are oodles of FM's available as the game progresses, going to war on a large scale typically dwindles down FM's quickly than anticipated, leaving towns abandoned.

I rely heavily on client rulers to ensure that newly conquered settlements are properly stable and managed. While expensive, having FM's in towns usually had great bonuses and stability in new settlements, and more importantly, free's my FM up to continue his battles instead of being bogged down in a newly conquered settlement.