There is no such thing as reloading modules in Perl. Apache2::Reload makes a pretty good try at it, but it can never work perfectly since there is no language support for this feature. Usually, I just restart the server when I make a change. It only takes a couple of seconds.
At my current job, we write code that works under both CGI and mod_perl, which means it works fine to run through CGI when you're developing, and then switch to mod_perl for testing and production. - Perrin