The Apple TV remote that comes with the latest Apple TV 2 is very small and can be very easily misplaced or lost completely. Luckily, Apple has included a very easy way for you to use a third-party remote control as an alternative. Sure you could use your iPhone, iPod touch, or iPad and the Apple Remote app but if you don’t want your kids, friends, or spouses, bugging you every time they need to change something on the Apple TV, you'll want something dedicated.
Here's how to set it up, and you should do it now before you lose your current remote.
If you see the "Button Already Learned" error message, this means one of the following:
Either use a different button or delete the previously learned remote if it is not being used.
That is all there is to it, a very easy way to use a third-party remote as a backup for your Apple TV remote!
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Source: Apple Support Article