I realize this is an old thread, and that the OP may not be tracking this anymore, but I wanted to help nonetheless.
I'm not sure how to do this in the Java version, but in the python version, what I ended up doing was creating a "fake" module and deploying this along with the normal app.yaml/appengine-web.xml.
What I did was:
1) create a file called fake.yaml (or something similar for the Java version; basically a copy of your appengine-web.xml but renamed to the name of your new module)
2) paste in the stuff from the top of your XML file, the stuff about 'runtime' and 'threadsafe'
3) within those entries at the top, write in a line that says 'module: fake' (or something equivalent in XML). I also included a handler entry for the favicon, just so that there's something that the fake module can route to.
4) now, back in your appengine-web.xml file, write in the scaling code, for manual or basic scaling
5) now open a Terminal/Command Prompt window and traverse to your app's directory
6) run the 'appcfg' command with the word 'update' followed by 'appengine-web.xml' and then the name of the XML file for your fake module.
In the python version, this looks like 'appcfg.py update app.yaml fake.yaml'
7) enter your email/password, then your application will deploy both the default module (configured from appengine-web.xml) and the fake module (configured from fake.xml or whatever the filename is)
This should enable the default module and enable any scaling you set. The configuration for the fake module doesn't matter, just so long as it doesn't error out when it updates. Feel free to delete it later.
Of course, if anyone knows of a better way to do this, please reply. After the research I did on this topic, this was the only method I could find.