TomEE specific configuration (ie not inherited one from Tomcat) is based on properties. Therefore you can fully configure TomEE using properties in conf/system.properties. However for convenience it also provides a hybrid XML alternative a.k.a. conf/tomee.xml.

Some settings can be specific to applications, these ones are also properties based and are read in WEB-INF/application.properties. When you can’t use tomee.xml to configure resources you can use WEB-INF/resources.xml which inherit from tomee.xml its syntax but binds the resources to the application and reuses the application classloader.

More about Container Configuration.