Can anyone point me to the steps/resources that describe:
First check this out if you haven't already ran through it:
http://docs.aws.amazon.com/gettingstarted/latest/awsgsg-intro/intro.html
it'll give you an idea of how it all works.
With regard to running a Java EE app on EC2, you have a couple of choices - but they generally come down to the following recipe:
Now you can bundle the above into an ebs ami, or you can write a script (bash/sh/tcl) which applies those changes when your instance starts (which i prefer). The scripts allow you to modify what gets installed/started/moved around without having to rebundle your instance.
There's some great resources here: http://developer.amazonwebservices.com/connect/kbcategory.jspa?categoryID=100
Hope that helps.