Thank you, Wolf, that was exactly the sort of thinking I needed to hear. I think I know exactly how to run those now, and how to work the rewards, and it is helping me with the overall story arc too.

In the original area free missions, you got discounts and new items depending on the number of free areas you had and the towns you freed. I was having trouble working enemy territories into that idea, since they are highly unlikely to want to give discounted prices to the enemy. However, if we run the area free missions as combat support missions for other attacking units, we can have an excuse to free areas that will never actually come under our control.

Due to Ivalice's lack of a true military force, the clans are the primary attackers in this war. This leads the Clan Center into becoming the primary HQ of the war effort in Ivalice. As you complete free area missions, the Clan Center will reward your efforts by reducing the price of shop items in Ivalice. However, the new shop items will be gotten in a slightly different way.

As everyone who has played FFTA knows, each Clan has its own home town (the Cyril Band is based in Cyril, etc...). Each of these Clans lost most of their influence when Clan Ultima freed their homes during the Clan Wars. Now these clans all pitch in to help the war effort, and they wind up needing help at certain times. And, as you help out a particular clan more and more, they will reward you with offering their items for sale in their hometown.