No, put them in run.conf at the end of the line starting with "if [ "x$JAVA_OPTS" = "x" ]" (if you are using unix/linux). So, it may look like:
if [ "x$JAVA_OPTS" = "x" ]; then
JAVA_OPTS="-Xms1303m -Xmx1303m -XX:MaxPermSize=256m -Dorg.jboss.resolver.warning=true -Dsun.rmi.dgc.client.gcInterval=3600000 -Dsun.rmi.dgc.server.gcInterval=3600000 -Dsun.lang.ClassLoader.allowArraySyntax=true -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Dcom.sun.management.jmxremote.port=8999"
fi
Then you can connect up remotely to this machine from jconsole. Like Wolf-Dieter mentioned, though, if you are using jconsole on the same box, you don't need to add these lines. If you start jconsole it will list the java processes you can connect to locally.