For the records: the official documentation, as for Spring Boot v1.2.0.RELEASE and Spring v4.1.3.RELEASE:
If the only change you need to make to logging is to set the levels of various loggers then you can do that in application.properties using the "logging.level" prefix, e.g.
logging.level.org.springframework.web: DEBUG
logging.level.org.hibernate: ERROR
You can also set the location of a file to log to (in addition to the console) using "logging.file".
To configure the more fine-grained settings of a logging system you need to use the native configuration format supported by the LoggingSystem in question. By default Spring Boot picks up the native configuration from its default location for the system (e.g. classpath:logback.xml for Logback), but you can set the location of the config file using the "logging.config" property.