There's no easy way to get two handlers of the same type with java.util.logging classes that have different arguments. Probably the simplest way to do this is to create a FileHandler subclass in your logging.properties that passes the appropriate arguments to enable your logging to take place, such as:
org.pkg1.handlers=java.util.logging.FileHandler
org.pkg2.handlers=org.pkg2.FileHandler
java.util.logging.FileHandler.pattern="org_pkg1_%u.%g.log"
org.pkg2.FileHandler.pattern="org_pkg2_%u.%g.log"
org/pkg2/FileHandler.java:
package org.pkg2;
import java.util.logging.*;
public class FileHandler extends java.util.logging.FileHandler {
public FileHandler() {
super(LogManager.getLogManager().getProperty("org.pkg2.FileHandler.pattern"));
}
}