To get discrete Stop, Play, Pause, Fast Forward, Rewind, Skip Ahead, Skip Back, Chapter Ahead, Chapter Back buttons working on your remote, read on:
Use the Apple TV "Learn Remote" Feature
1) On your Harmony remote, add a remote profile for a DVD player you do not own and that does not conflict with your current setup.
2) Go into Settings -> General -> Remotes
3) Click "Learn Remote"
4) Click "Start"
5) Follow the on-screen instructions to learn each individual button available on the basic Aluminum remote. Simply press and hold the button on your Harmony remote which you want to perform each function. Bear with me!
6) Once setup is complete, press down on your now working Harmony remote and choose Setup Playback Buttons
7) Again, follow the instructions to set up the following commands:
Play
Pause
Stop
Rewind
Fast Foward
Prev Chapter
Next Chapter
Skip Ahead
Skip Back
8) Profit.
You can do this as many times as you like, for multiple remotes. If you have a sound system remote with a little switch on it that shifts between System/DVD/TV etc you can flip this switch to DVD and follow the above tutorial to roll your volume control/AppleTV2 control into one remote.
+1