In Sins of a Dark Age the Commander is responsible for managing the high level tasks and strategy such as base building, defense positioning, scouting, supplementary resource acquisition, army building, army control, timely use of your specific Commander's Realm Powers and more. You choose your Commander type at the beginning of the match and he/she does not have a 3d avatar in the game session. Heroes are responsible for supporting their Commander's army in battle, annihilating the enemy Commander's army, assassinating enemy Heroes, collecting additional resources and much more depending on the specific Hero type. You choose your Hero type at the beginning of a match and he/she is represented by a fully controllable avatar in the game session.
Source: Wikipedia, "Sins of a Dark Age", available under the CC-BY-SA License.