Normally, you create modules with h2xs or its modern equivalents: ExtUtils::ModuleMaker or Module::starter.

For a module Foo::Bar, this will create a template module kit under ./Foo/Bar including a MANIFEST and Makefile.PL (which makes use of ExtUtils::MakeMaker). Your module Bar.pm itself can either live in ./Foo/Bar or in ./Foo/Bar/lib/Foo, which is where to put it if your module kit aims to deliver nore than one .pm module.

This directory tree (no version number) is what you should check into the VCS.

Inside the template Bar.pm will be a line which defines $Foo::Bar::VERSION - this is where WriteMakefile (in Makefile.PL) will get the version number from. make distdir will generate a directory tree with a version number on should you need one.

See also How to make a CPAN Module Distribution

Hope this helps