To make a project like that, first create the toplevel project with:
M-x ede-new RET
and fill it in as an Automake or Makefile based project. (either is fine.) Then for each sub-directory, use ede-new
again with the same project style. These projects will get linked together under the top-level project. You then use
M-x customize-project RET
to edit any features you need for the project. If you use dired, you can mark files and use the Project menu to add those files to some target, or create new targets to add them to. You don't need to know what is in the Project.ede files to do that. As it happens, the Project.ede file is just some Emacs Lisp code that creates the objects that represent the project you are working in.