With Eclipse debugging an ATG application running on JBoss is fairly straightforward.

1. Configure JBoss to start up with Java options for debugging.

   On UNIX you do this by uncommenting this line in <JBoss>/bin/run.conf.

   #JAVA_OPTS="$JAVA_OPTS -Xdebug -Xrunjdwp:transport=dt_socket,address=8787,server=y,suspend=y"

   On Windows you do this by uncommenting this line in <JBoss>/bin/run.bat.

   rem set JAVA_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,address=8787,server=y,suspend=y %JAVA_OPTS%

2. Create a remote Java application debug configuration using the port you specified in step 1.  The default port is 8787.

For further reading please see Debugging Nucleus components in JBoss with Eclipse or Remote Debugging with Eclipse.  There is also a very complete tutorial from O’Reilly Media called Configuring Eclipse for Remote Debugging.