The EC2 instance is associated with a Container Service cluster using the /etc/ecs/ecs.config file on the instance, in the format ECSCLUSTER=yourcluster_name.
The EC2 instance must also have the ECS agent installed. If you create the instance using the ECS AMI this will be pre-installed (search for AMI called amazon-ecs-optimized).
This configuration can be put in the User Data field:
echo ECS_CLUSTER=your_cluster_name >>/etc/ecs/ecs.config
To find the setting on an instance that already exists: Actions -> Instance Settings -> View/Change User Data
Exact instructions for setting up the EC2 instance properly can be found here: http://docs.aws.amazon.com/AmazonECS/latest/developerguide/launchcontainerinstance.html