In the "advanced search" section of the log viewer, you can select (or edit) the list of logger you want to display. It is therefore very easily to display only the logs of your application, even if they are in server.log.
If you really want to have separate logs, you can configure your logger either programmatically during startup, or declaratively with a configuration file, or write a custom handler. See
http://forums.java.net/jive/thread.jspa?messageID=247074
The log viewer will list all the files in the "logs" directory. I you place your own ones there, you will be able to view them with the log viewer.
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