Taken from the Mac Rumors forum.
Ok I just spent 12 hours (there was some sleep in the middle there) getting my Harmony 676 remote to work properly with AppleTV. In the end the setup proved to be quite simple and it (finally) works perfectly. I figured I’d post my guide to save all you folks the tedious trial and error pathway I had to go through.
I figured it would be simple just to do a learn IR command for each of the settings but that never worked properly and the remote just wouldn’t sense the commands. When it did, the IR response for the apple TV was sluggish or very sketchy.
The trick is to just add a new apple computer device and then have your activity reference it for the buttons. I also changed my delays to 100ms.
Ok here’s the step by step to save everyone some time
1 In your harmony Remote Software Click “Add Device”
2 Click “Computer”, next, next
3 Select “Apple”, next
4 Now type in EXACTLY “Mac Mini 1.66GHz Intel Core Duo”, next
5 Check “do not have a remote” and hit next again
6 All info correct, next
Back to Main Screen
1 Click on the settings button for “Computer”
2 Click adjust delays
3 Change delays to 100 ms, done
The activity setup is done, if you want to be fancy, you can rename it “AppleTV” knock yourself out.
Now go to the Activities window
1 Click on add new activity
2 Manually add
3 Click “utility”, next
4 generic activity, next,
5 Add or Remove all the devices you do or don’t need. Make sure to leave your TV, computer/AppleTV, amplifier or any other devices you use while the AppleTV is displaying, then hit save
6 Video 6 for me (your settings will vary), next
7 don’t need to set, next
8 amplifier input for me is video 4 (again your settings will vary), next
9 next next done
Please rename your activity from custom to AppleTV etc
Ok Now you have to assign the correct AppleTV buttons to the remote
1 Click on “customize buttons” for the AppleTV activity
2 Just go down and select the “AppleTV” for the device, and the appropriate commands. I also set Menu, A, B and the guide buttons to the AppleTV Guide so I could hit any of them to go backwards. Set your Volume up, mute and volume down to be controlled by your amplifier/TV. I set my left and right direction buttons to skip forward and back as I wasn’t sure if the rewind and fast foward buttons send a longer IR pulse…
3 Click done and you’re as good as gold.
Oh, forgot one last thing, you have to unsynch your AppleTV remote and synch the harmony (by clicking the play/ok button) for the AppleTV to recognize the harmony.
Hope that speed’s things up for a few people. I set my little music button on the remote to my AppleTV activity.