Okay team, so I figured this out.
First off on my set up the apc.ini file resides in the conf.d directory deep inside my /etc/php5/cli directory. I have know idea why it's there, but this is the place. Anyhow, because I installed php_apc as a module (apt-get install php_apc) it uses the predefined apc compiled in settings which is why I was seeing the variables in dump out when I ran php -i. Okay to override any of these variables I just needed to add them to this almost blank file and it worked! Great!
As far as how to enable apc.php. This file is bundled with http://pecl.php.net/package/APC so don't make the same mistake I did and try to keep accessing the /wp-content/plugins/w3-total-cache/pub/apc.php via your browser because that is not the same file and will not work. Anyhow, just upload the apc.php from the APC Package and your ready to rock. You should be able to view it from http://www.yoursite.com/apc.php
That's about it for now.
Philip