This is not for the experienced JBoss application server user. It is meant to  give the JBoss beginner the basics to running and deploying applications to  JBoss 4.0.3 SP1.
 JBoss Layout
JBoss is easy to understand if you know the way the  directories are setup and how to work with them. First everything you will do to  JBoss is in the install directory.  
bin directory
The most important one here is the run.bat or run.sh. This  will run the application server and display debug and information messages to  the user in the session it is started in. To start JBoss simply use the run  command from this directory. To stop the server do a CTRL-C in the session it  was started in. There are also some other files there but this is the basics  only so I will not discuss them.  
lib directory
This is the "root" server lib directory. You don't usually  have to nor want to do anything with these libs.  
server directory
This is where the directories for the server instances  are. This is where you will do most of your work.  
default directory
The default directory is the directory for the default  instance. This is the instance which is started if you do not specify an  instance. If you are in need of multiple instances then you will need to  duplicate this directory. So if you think that you will need more instances do  yourself a favor and make a backup of this directory before doing anything else.   
I will go through this directory and tell you a little about it and give you  a little information which may come in handy in the future. 
 conf
This is where all the configuration files for the paticular  instance reside. These are more or less needed but you don't need to do much  with them to work with the server. The only one I have changed in this directory  is the log4j.xml because I wanted to add some different appenders to keep more  concise logs.  
data
This directory I have never done anything in and never even  navigated to tell I decided to write this. The only think I could see of any  interest is the wsdl directory which will hold a sub directory for each archive  which holds a web service which holds the wsdl and wsdd files for each service.  
deploy
This is the most important directory. It contains all the  deployed applications archive files and the jbossweb-tomcat55.sar directory. The most important thing in the jbossweb-tomcat55.sar directory is  the server.xml. This is the file which will need to be modified if you are going  to have multiple instances running. If you do run multiple instances make sure  you change the listening ports in the server.xml, refeer to the 
JBoss  site for information on changing ports. To run a server with a different name  use this command run -c 
instance_name. The next important directory is  lib. It is where the archive files need to be put for the instance to find them.  For instance if you are going to be using databases the database lib goes here.  The log directory is next, it is where the logs for the instance get put. The  temp and work are where the applications get expanded to and run from.  
others
There are other directories but these are all you really need to  worry about when getting started.  
JBoss Deployment
Since JBoss hot deploys new applications it  works very will for me. I simply build the project and then use a script to  deploy it from a command prompt.
Source: Dru Devore's Blog