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). 

• <projectName>
  • integration
    • src/main
      • java
        • com/squidpower/sray/<projectName>/integration
          • dao – for data access objects
          • value – for value objects
          • delegate – for web service or remote objects
          • assembler – for flex data services assembler objects
  • presentation
    • src/main
      • flex2 – contains mxml and action script files
      • java – contains presentation related java code (e.g. struts actions)
      • webapp – contains WEB-INF and html, jsp, etc.