I want to use java logging for my jsp applications. I managed to configure java logging by an logging.propeerties file that I placed in the application's root directory. Then I deploy the application into Tomcat and everything works fine. The application produces a log file with its name and logs into it. When I deploy a second application with a different logging.properties file into Tomcat it overwrites the configuration of the first application. Both applications now log into the file of the second application.
I bet you are using the same Logger instance for both applications. You need to create independent Logger instances and configure them to write to seperate files. The name you pass to Logger.getLogger() determines if you get an existing Logger:
Loggers are normally named, using a hierarchical dot-separated namespace. Logger names can be arbitrary strings, but they should normally be based on the package name or class name of the logged component, such as java.net or javax.swing. In additon it is possible to create "anonymous" Loggers that are not stored in the Logger namespace.