Most of your confusion is, I suspect, due to the page you linked advocating 1.2.3 style version "numbers". These are not fully supported throughout all the toolchain (regardless of what others may say) and should not be used. They offer no advantage over a simple numeric version, since they must for compatibility be treated as just a number in many places (e.g. 1.2.3 is treated as 1.002003). Oh, except that they are "cool". And maybe "elegant". And obnoxious.
The correct way to declare a version number is simple, unless you have an XS component or a alpha/beta indicator (_ in the version number), since then some things need to see a version string and some things a version number. Then it gets more complicated. perlmodstyle provides the correct incantation:
If you want to release a 'beta' or
'alpha' version of a module but don't
want CPAN.pm to list it as most recent
use an '_' after the regular version
number followed by at least 2 digits,
eg. 1.20_01. If you do this, the
following idiom is recommended:
$VERSION = "1.12_01";
$XS_VERSION = $VERSION; # only needed if you have XS code
$VERSION = eval $VERSION;
(This assumes $VERSION and $XS_VERSION have already been declared; if not, simply add our
to the first two lines.)