I'm using one system folder for all CI apps I have on my site. For some reason, I need to have scaffolding in my application folder, not system (every app should use it's scaffolding instance).
[eluser]danmontgomery[/eluser]
The scaffolding trigger is set in ./application/config/config.php, and enabled in the controller, so you just set a trigger in each application's config and enable it in whichever controllers you want