Till now I have been coding in Java.
Wanted to know - what happens after deployment in Application Server
Suppose I deployed my EAR in AppServer (WebSphere or Jboss and Assuming Deployed Successfully!)
Is there any document or anything ?
That is a VERY VERY vague question, I would start here: http://pic.dhe.ibm.com/infocenter/wasinfo/v7r0/index.jsp with the instructions for WebSphere Application server v7 "Developing and deploying applications" section.