I think there could be a Strat Level of resources that you get from holding territories and winning battles, and then you can translate those resources to upgrading your territories and choosing bigger amounts of starting resources for the next skirmish match.
So, let's say the campaign map is Greece/Aegean/Asia Minor. The Campaign resource could be called "Talents." It's a nice neutral, but historic money designation. Each territory you hold could either grant you more talents or cost you talents. Holding Laurium, for example, where historically there was a very famous and productive silver mine, would grant you talents, but holding Marathon would be neutral or cost you talents. What you use talents on is you could buy starting buildings for each territory. So, if you erect a Storehouse in the Marathon territory you'd start any skirmish in that territory with a free Storehouse. Buy a garrison with your talents and that territory will start with extra soldiers or defend itself against an enemy attack even if you have no Hero or General there. The enemy could take it before you get there, but it would be costlier for them to take it in deaths.
You could even "store" talents in specific territories so that you start a skirmish map there with extra resources.