For example, if your main MXML file is Main.mxml and your code-behind class is MainClass.as, Flex Builder gets confused and thinks that there should be two application configuration files (one for the MXML file and one for the AS file.) If your app.xml file is named Main-app.xml, you'll get an error along the lines of Adobe AIR application is missing the corresponding MainClass-app.xml.
The Flex client works exactly like the Flash 9 client and shares an almost identical codebase. 99% of the framework is the same.