Harmony supports the Apple Remote out of the box. I believe AppleTV is one of the "media center" devices, and the codes it sends to it are Apple Remote codes. Call your Mac an AppleTV and all works as you would expect (FrontRow is essentially AppleTV's Finder, so ...) The only catch is pairing/unpairing; there's only one identifier that Logitech ships with, so you couldn't for instance pair one Harmony remote with your ATV and another with your MacBook and not expect crosstalk. That should be the ONLY time you'll need to worry about manually teaching the Harmony Apple Remote codes.
Originally Posted by Septimus
I had serious reservations about the Harmony for years, wondering how well it would react to the system getting "out of sync" with the remote. Got one about a year ago (a 680 I believe), and absolutely love it. It's a great remote! And, oddly enough, took less than a quarter of the time to configure than my previous clunky uber-remote (primarily thanks to using my Mac to set it up rather than trying to key things in on the arcane remote interface).
Running Boxee on AppleTV since Oct '08.
Boxee v0.9.11.5591 / ATV v2.3.1 / Launcher v3.0