[Desktop] Background app code

Based on my research the typical advice on how to create a desktop background app in AIR is essentially:

// when the app loads
NativeApplication.nativeApplication.autoExit = false;
stage.nativeWindow.close();

That closes the window but keeps the app running... but how do I continue to execute code, then? Since my main window is the Document class, won't closing that window result in that Document class instance being GC'd? How/where can I continue to run code, handle events, etc?

-Aaron