I would like to add the Log4Perl configuration into the very same xml files, but I have not really understood how I could do this.
If you have a collection of XML files to configure your application, just add another configuration file for Log4perl to the collection.
Now, you can configure Log4perl in XML or in the native Log4perl format. I personally dislike XML because it's hard to read, so I use the standard configuration format as explained in the Log4perl manual pages.
If you really want to embed the Log4perl configuration in your configuration format, you're gonna lose useful features like init_and_watch(), but you can do that by parsing out the configuration, storing it in a hash and passing it to init(). See the section alternative initialization in the Log4perl manual for details.
But again, I'd recommend using the standard way with a separate configuration file, it definitely has its advantages.