Huh, this plugin sounds like a sploggers dream... but anyway...
Download the latest version from http://wordpress.org/extend/plugins/wp-o-matic/
Edit wp-content/plugins/wp-o-matic/wpomatic.php and change line 394 from
to now read
WPOTools::getBinaryPath('curl', ' -U proxyuser:proxypasswd -x proxy:8080'),
Change proxyuser, proxypasswd, proxy, and 8080 to the appropriate values.
I'm guessing you have curl on your system. When you setup the plugin if it finds curl and you make these edits, then you'll see it in the generated config.