The directories under server (server/all, server/default, server/minimal) represent three different configurations of JBossAS. You probably are using only one of those. The one you are using is specified on the command line. For example, if your start JBossAS using:
run -c all
then you are using the "all" configuration (directory server/all). If you do not provide any configuration option:
then you are using the "default" configuration.
When changing any files, such as log4j.xml, you need only change the one that is in the configuration(s) you are using.
If you want to create a new configuration, based on default, is it best to simply copy the default or is there some kind of tool to create a new config?
There was the JEMS installer which was meant to allow the user create a configuration of his choice. But based on what i have seen in these forums, the JEMS installer has bugs and its recommended that you use the "copy" approach to create a new config.