The files provided here can just be overwritten on top of an existing, vanilla CI application. PHPUnit's phpunit.xml will sit besides your application's index.php, and hacked CI's system/core files should overwrite the vanilla CI ones.
After that, just put your own tests in application/tests folder. Utility classes CITestCase.php and CIDatabaseTestCase.php are provided to be used instead of PHPUnit_Framework_TestCase, but you can use PHPUnit's standard classes as well.
As an example, a unit test for CI's Email helper would be as follows: