Here is a quick and dirty answer.
JBoss follows the J2EE spec, so you put the application code and deployment descriptors in a .ear file and typically this .ear file goes into default/deploy. If you have classes that are common across applications (across .ear files) you can jar these classes up into their own jar file and put it into default/deploy. You can put these jars into default/lib, but then they would not be available for hot redeploy. Don't put things like crimson.jar into your jars, as these things are universally available to your app code. Things usually put into default/deploy and also be put anywhere on the web and referenced via a URL. Either hardcode this URL in the default/conf/standardjboss.xml or after JBoss starts up, go into the jmx console and add the URL in the deployment MBean.
Anything beyond that, you probably should browse at least the QuickStart Guide and get a copy of the Admin Guide, all available from the documentation page.