Personally, I would separate 'A' and 'B' projects into two separate distributions, and then lay them out like this:

  MyDist::A root directory/

     Makefile.PL
     README
     CHANGES
     MANIFEST
     MANIFEST.SKIP
   
     lib/
        MyDist/
          A.pm
          A/
             A1.pm
             A2.pm
 
     t/
        test1.t
        test2.t
        ...
[download]

In A.pm, you'd use MyDist::A::A1; and use MyDist::A::A2; to pull in the helpers. If you do want just a top-level namespace, just remove all references to MyDist.

That's consistent with how most CPAN structures are laid out, so I'd stick with what works.