Can anyone point me to the steps/resources that describe:
How to deploy a Java EE app on amazon-EC2
You still deploy to an application server so it isn't really different. If you have more specific questions, please clarify. But have a look at Running JEE applications on Amazon EC2 and How to deploy a java web application on an ec2 instance.
Maintain changes to the meta-data of the app server (deploy new applications) after an instance reboot (probably using amazon-ebs)
If you use Amazon EBS, then you don't need to worry, Amazon EBS volumes are off-instance storage that persists independently from the life of an instance.