Aside from controlling them one at a time, you can also give order to your AI allies: either ATTACK or DEFEND.

To give orders to your AI allies during a game, look at any building and search for the icons with crowns on them. Tapping on a blue icon, which are close to blue buildings, will order your allies to Defend this building, while tapping a red icon, which are close to red buildings, will order your allies to Attack it.