On the settings page for Better Click To Tweet, simply check the box indicating you'd like to use the short URL, and save changes. If you've got a plugin that correctly hijacks the built-in WordPress shortlink functionality, you're all set!
I've also written <a href="http://benlikes.us/79" title="shortlink tutorial">a tutorial</a> for how to set up the shortlinks with bit.ly and yourls.org.