Before Deploying Troops
Don't rush to deploy troops, focus on destroyng enemy offensive buildings first with Missle skill. If your Missle skill does not deal much damage you may need to consider upgrading the hero to enhance the skill.
Deploying Troops
Once you have deployed your troops use the Locate skill to guide them to destroy any remaining offensive buildings.
More Morale
You can get more Morale (blue cube) by destroying enemy buildings, just make sure you avoid casualties by guiding your troops to bypass any mines.
Enemy Headquarters
When you have destroyed all the enemy offensive buildings move your troops into position to attack the enemy Headquarters. Try to win the battle without destroying other buildings.
Direct Attack
If you have enough troops and are not concerned about casualties you can always stage a direct assault of the enemy Headquarters from the beginning.
Difficult Stages
When you encounter difficult stages you need to ensure you take a large army and more heroes to battle.