using both uri segments and query strings in 1 app

[eluser]skibum001[/eluser]
I am building a facebook app that has some of the functionality of my web app. As such, I want to re-use all my models and a number of views in the facebook version.

On my web app, I am using CI's lovely uri segs but as the facebook app will use a fair bit of JS, I need to use their iframes which meaning lots of facebook style query strings getting appended to the URI.

So my question is, how do I use both?

I have different controllers for my web app and facebook and tried using $this->config->set_item but this didn't work (I am guessing because CI determines uri types before getting to my contoller).

Next I tried to hack index.php and codeigniter.php but without luck. I created a new /facebook/ dir which had index.php, codeigniter.php, common.php and config.php and which changed the basepath and apppath to these locations but left the basepath and apppath to everything else the same. When I try mysite.com/facebook/index.php all I get is a blank screen (previously I got error messages until I fixed the errors). mysite.com/facebook/wrongurl loads my custom 404 page perfectly.

How do I make this work? I only want query strings to work in the /facebook/ directory.

Thanks for your help.