This article describes the logging configuration starting JBoss AS v7.0.0. The article should be updated periodically with any changes that have happened to logging (and note the version where the change occurred).
Boot Logging
This is the boot.log that you see. Its configuration is in the logging.properties.
Server Logging
The configuration should be done in the standalone.xml for the standalone distribution. Basically the configuration now is done in the domain model. So it is either domain.xml or standalone.xml depending on the type of distribution.
The log output will go into server.log
Deployment Level Logging
This is when you want to have your own JDK or Log4J logging driven at the deployment level. This feature needs to be implemented by https://issues.jboss.org/browse/JBAS-9084