Use (almost) any remote with an Apple TV - While the small, sleek aluminum remote that comes with the Apple TV is nice, it may be one too many. The Apple TV can work with many other infrared remotes, and an Apple technical document outlines the procedure for having the Apple TV "learn" your remote.
You'll need to use the Apple remote to set this up, and you do so by choosing Settings > General > Remotes from the Apple TV's interface. Choose Learn Remote, and press the six buttons that the Apple TV needs to learn.
Some remotes may not work, so read Apple's technical document for more information.