In addition to the cool, space-age aluminum remote bundled with the ATV, the ok iPhone Remote app, and the awesome iPad remote app, there is another option. In the remote control settings page of the Apple TV lies a feature that allows the device to learn the codes from pretty much any other remote you might have laying around. It's sort of like a reverse learning remote control.
Now here's the trick, the remote control
The links below will walk you through the steps necessary to set up each device.
TiVo support article for controlling multiple devices with one remote.
important note: when performing step 5, DO NOT point the remote at your TiVo (go to another room or keep the remote covered) otherwise you will simply change your TiVo to use the DVR 2 IR codes.
Apple support article for "learn remote" feature of Apple TV 2
Final note, if you lack the 1-2 switch on your remote, in addition to the sponsored links above, you can purchase replacement remotes (and pretty much everything else TiVo related) from weaKnees. I am also not totally sure if the older style remotes that have this switch can can control a Premier unit or not. They work fine for everything from the Series 1 to the HD units I've had.