Buh... forgive me for only responding in terms of theory and not in terms of practice, because I understand the concepts underlying what you're trying to do, but lack directly applicable experience with either set of the Selenium2 webdrivers.
With respect to what you're trying to achieve, however, it seems comparable to any asynchronous set of operations on multiple internet windows and therefore should be something you can handle thusly regardless of which programming language or tool set is employed.
Just glancing over the API documentation, it appears that the tools used for these types of events are the "andWait" / "waitFor" methods: http://seleniumhq.org/docs/02_selenium_ide.html#the-andwait-commands
Since you didn't provide much detail as to WHAT you want to do with multiple windows, let's assume for a moment that your application wants to play tic-tac-toe in two windows, and one of each window is responsible for playing the side in question.
So. once you have successfully created a Selenium instance that can do ONE side of what you're looking to accomplish (check out http://seleniumhq.org/docs/03_webdriver.html for more webdriver docs -- I'm seeing everything you need there to get most jobs done), it simply becomes a matter of keeping both sides in sequence. You can run both jobs simultaneously and have them report back to a service daemon you create specifically for this purpose, tracking based on time stamps or other sequential data YOU provide arbitrarily to keep the events of each browser window "in step" with the other one.
Again, I can only respond in basic theory because of the limited amount of information I have on your project and my limited experience with Selenium; however, I hope this helps.