how to arrange source control?

If I have all my (source and executables) under one directory, like:

rootdir
   libs
      lib1
      lib2
      lib3
      ....
   app1
      release
      debug
      data
      ....
   app2
      ....
   app3
      ....
   ....

what is the best way to use git? Should I run "git add ." in 'rootdir' or run it in each application and library? These libraries
are used by all of the applications.

thanks,
Bob