Troops:
recruiting probably based on mercenary camps. But it may be converted to training units if there could be AI problems, but somehow limit they training. They could wander around like in homm4, but can't capture mines or towns. But under a hero they would get more benefits (using various auras etc). However one possibility would be to give them to an allied computer player so they just follow the hero. About the stack I didn't though, that would be hard to do, still I prefer age of wonders style to be based on (that game is easier to convert to RTS).
Resources:
Gathering resources would pretty straightforward, resouces gained regarding how many mines do you own, which are capturable like a town (that flag). I was thinking to add also food as one one of resources, so units won't have that food cost as population. This would require some triggering.
Just this is how I thought to do, maybe I can write more later.