The deal with jakarta commons-logging (JCL) is that it uses whatever underlying configuration files it can get it's greedy paws on.
So, for example, if you put log4j.jar in your classpath, and supplied a log4j config file, then JCL will use that configuration (as best it can).
I'm a huge fan of log4j myself, so I'd recommend that package.
If you don't want to use that, and if you're using JDK1.4, then JCL will attempt to use the logging config the the jdk's java.util.logging package. I've never used that one, but I understand you can configure it a number of different ways. Not sure if you can do so *through* JCL though (probably not though).
finally, if you don't have log4j or jdk1.4, you get down to JCL's SimpleLogger, which it looks like you have to configure through system properties? That doesn't seem right though.