Well the way i go about it , wil be using Xdoclet for thta, which will generate the DD (deployment descriptors) and relavent code files.
as compred to devloping the application on SUN tools a u have mntioned u will find that this methodlogy drastically reduces the devlopment time and generates thd DD for u and u can see what is being generated and where.
As far as sructure of jar and war file is concerned it remains same.
Only addition is u have jboss.xml file in yr ejbxxx.jar file alongwith ejb-jar/xml and inw webxxx.war file u have jboss-web.xml file in addition to web.xml.
These two files are appliction server specific as each application server does have some conffiguration issues and others.
Also u have to be careful for JNDI names, esp in case of databases.
Another one to look after is where yr naming server is listening which goes normally in to client side in properties file as in jboss it listens on jnp:\\1099
Also have a loolk t this tutorial, which covers if u have to learn the path of Xdoclet.