I have developed a quite complex software with derby embedded into it &
access to data through ejb3 ( toplink

)RUNOPTS="-Dconfig.filename=project.base.xml -Dconfig.location=file
-Dderby.system.home=/home/java/databases"

java $RUNOPTS tibetsoftware.wenmei.core.Main 2>&1 | tee LOG

you can put the derby database folder anywhere you want it to be
simply need to setup some sort of environment like
you can even start the database within java

serverThread srv=new serverThread();
        srv.run();

package tibetsoftware.wenmei.core;

import java.net.UnknownHostException;
import org.apache.derby.drda.NetworkServerControl;

public class serverThread  extends Thread {

    public void start() {
        System.out.println("Starting Server Thread...");
        try {
            NetworkServerControl server = new

            // hostname/port read from derby.properties
            NetworkServerControl();

            // hostname/port as arguments
            //NetworkServerControl(InetAddress.getByName("9.x.x.x"),1527);

            server.start(null);
        } catch (UnknownHostException e) {
            System.out.println("Unkown host error");
            e.printStackTrace();
        } catch (Exception e) {
            System.out.println("Unkown EXCEPTION");
            e.printStackTrace();
        }
    }
    public void run() {
        start();
    }
}

hope that helps
patrick