How to organize applications ?

To be safe use your own namespace name for your own company.

CompanyName
-- ModuleName
---- Controllers
---- etc;

You mean that way ...

CompanyName (my Namespace)
  +Backend_Modul
      + Modul_A
      + Modul_B
  +Frontdend_Modul
      + Modul_A
      + Modul_B


But i have also to build a namespace (subnamespace) for the Backend_Modul and the Frondend_Modul, or ...?