Yeah, it's a flat fee to take over an enemy merchant. I tend towards 'fire and forget' merchants. I train 'em at the best facility available, target them at a distant resource, and forget about them unless I happen to see them get blocked or knocked off.

There are a few resources I always take over and dominate though, even if it requires some micromanagement. The gold east of Zagreb, the textiles around Constantinople, and everything between Antioch and Damascus.