Question:  How do a use a custom server.xml with Tomcat in JBuilder 4,5 and 6?

Answer:
Make a copy of the JBuilder-generated server.xml file while your Web app 
is running, modify the line which says the file was generated by JBuilder,
make you mods, and then AFTER you quit the Web app you were just running, 
save your modified copy back to server.xml. After that, JBuilder won't 
modify that file.

Note: Remember that when you shut down Tomcat you'll need to recreate 
the directory that the server.xml file was in before you can save it back out. 
After you've made the above modifications, JBuilder will leave the directory 
alone.