I have used the installer (patch 1) to setup a configuration of JBoss which use 'all' and 'ejb3'. That is to say that I first setup jboss with the 'all' configuration and then setup jboss with the 'ejb3' confiiguration. I use the same configuration name for both setups.
I hope this is the correct procedure, but I am not sure if this is what is meant at the download page:
If you want to use EJB3 or Seam, you MUST download the xxxx-installer.jar installer file. You need to run the installer by double clicking on it or executing java -jar xxxx-installer.jar. Choose the ejb3 or ejb3-clustering profile when asked. JDK 5.0 is required.