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It sounds like you are simply dealing with one main app and mxml (or AS) components used by the main app.
In this case it is easy, child app accesses main app using Application.application.myVariable or Application.application.myMethod (don't forget to import mx.core.Application).
If the apps are both distinct "main apps", use LocalConnection (see FB3 help).
Oh, and if you want the main app to access the child app, just use the identifier in the main app:
var myChildComp:MyFancySmancyChildComp = new MyFancySmancyChildComp();
Also, be careful with your terminology.
If you are using popUpManager, then you do not have an application and a "child app", you have a single application and a component.