IIRC if you don't have XS modules, you can move the whole module tree into a lib subdirectory of the distro tree with the full path you'd eventually want them to have (i.e. My::Module into lib/My/Module.pm) and your Makefile.PL should pick all of them up. You may need to adjust references to the main module in Makefile.PL when you do that: 
Makefile.PL
lib/X.pm
lib/X/Y.pm
# etc ..

[download]
Many modules on CPAN do this. Simple example: my Text::PSP module.

If you do need XS code, the only way I've found to make that work is to put each XS additional module in its own subdirectory immediately below the main dir together with its own Makefile.PL (they'll be used automatically when you use the top-level Makefile.PL)

"What should it profit a man, if he should win a flame war, yet lose his cool?"

In reply to Re: Building a CPAN module by Joost
in thread Building a CPAN module by true_atlantis

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