I was lucky enough to come across a blog post on Binary Moon that included a function that would allow you to break up the trackbacks and the comments in your template. [...] The problem with that is everytime Wordpress upgrades I overwrite functions.php and then comments no longer work.

To get around it, he used WordPress' own plugin system to make the separation via this simple plugin [zip]. It's a simple install, but a bit of functionality that can really help out if you get a lot of both trackbacks and comments.