This blog describes a proposed directory structure for web applications that contain a mix of flex applications, java presentation layer code, and java integration layer code.  From this structure you could easily build projects using ant or maven (preferred). 

Here are the short and concise reasons why maven is a better choice than ant for project builds:

Maven can run any ant scripts you need, so maven can do any thing ant does.
Maven does not need to be explicitly told to compile java files or build a war or ear file, so there is less […]