It has been ages since I did anything with WLS so I won't comment there.
But with JBoss AS, the sane way is to edit the xml configuration files directly. With most changes, a restart is required. There is also an admin console but not all changes made through it are persistent (you lose them on the next restart).
Actually, I answered the question regarding configuration, not administration (which includes configuration but also encompasses monitoring and other activities). For that Jopr is good. And then there is the JBoss Operations Network (JON) for EAP (the enterprise version of JBoss AS).