One of Flex’s greatest blessings is also its biggest curse: it’s quick & easy to throw together a working app. The problem which needs to be avoided though is that it’s too easy to end up with huge mxml files which contain all of the application logic.
If you’re looking to understand how to architect your application I can’t recommend strongly enough reading the Cairngorm 3 documentation.
The name is a bit misleading. Rather than being the next version of Cairngorm (which was the first major Flex framework) it’s a collection of best practices along with a set of libraries which guide developers to build scalable applications.