Here is what I've always done:

h2xs -X -A Foo::Bar
h2xs -X -A Foo::Bar::Baz
h2xs -X -A Foo::Bar::Quux

Then assuming that 'Bar' is your package ( i.e. Baz AND Quux will always be built and installed together ) you need to do a 'make manifest' in ./Foo/Bar

MakeMaker will automagically traverse the directory structure on build, the 'make manifest' simply makes it easier to package ./Foo/Bar/* into a .tar.gz with a 'make dist'

You won't have a ./Foo/Bar.pm because h2xs creates a directory for each module. Hope this helps.

-----------------------------------
Frank Wiles <frank@wiles.org>
http://frank.wiles.org