In your build.xml file, simply have multiple <javac> elements for each source dir. Have them all compile to the same class folder. That way, when it comes time to put them into a JAR or WAR, you can simply treat them as a single unit. You may have to set up classpath parameters appropriately so that the interdependencies ebtween the different source directories get worked out, but I've done it and it works great.
Jon Emerson
http://www.jonemerson.net/