Divide the troops under the players command by unit type.
Determined the amount of troops in each unit. Each of those units has a commander. If you want, you could delegate that the units have hit points equal to the number of troops in the unit.
During battle, the player commands the units to do what they need to do on the battle field.
If I was running this for 4e I would use the monster creation rules and create the units utilizing the role model:
Artillery for archers
Skirmishers for Light Units/Calvary
Soldiers for Heavy Calvary
Lurkers for Spies/Assassins/Snipers
Brutes for Footman
Controllers for command units or units containing wizards, etc.
You can give each unit some specific powers they can do that effect the battle field.
Units have to target other units. Players can split the units, provided they have a commander, halving the hit points. But splitting should also effect the damage output, perhaps giving them the weakened state. When units get bloodied they have a chance of being routed and should be given a 2nd wind to reform. They can also be replenished by healers and reinforcements, two units of the same merging.
You have a lot of options to play with.
Personally, if it was for 4e, I would make the battle a skill challenge rather than actual combat.
Some sites on medieval warfare