The first thing to do is to work through all the examples on the Wiki page.
As Mark pointed out, you put Log4J settings in log4j.properties or a log4j properties file extension.
Once you've gone through the Wiki examples, you should have a better idea of the APIs available. In the old audit mechanism, there were no Alfresco-supplied APIs to query the audit data - hand-cranked SQL was required. Now, the WebScript APIs provide that functionality and hand-cranked SQL is out. Of course, you can use the AuditService Java API as well.