Every soldier has different skills, strength, and weapons. Use them strategically to win the battle. The different options are shown on the active warrior, LEFT CLICK on them to perform the desired operation.
Your aim is to position your mechanized soldiers on the battlefield and attack the enemy troops using different weapons.
GameSpot's Game Guide to Twilight Princess has a full walkthrough, with videos for each boss fight, as well as a list of all the Pieces of Heart in the game!