1) Quit Remote Buddy (important - OS X will otherwise just rewrite the pref files when you quit it!)

2) Move the pref files located at ~/Library/Preferences/com.iospirit.remotebuddy* to another directory

3) Move the Behaviours you created from ~/Library/Application Support/Remote Buddy/Behaviours/ to another directory.

That's it, really.

Please be aware that the Harmony Remote often doesn't correctly learn Apple Remote codes and just replays the raw IR signal. For a single button press, the Harmony remote will then send multiple button presses., which can lead to undesired effects.

I therefore strongly recommend you to use a real Apple Remote or the pre-defined Apple Remote profile by Logitech while you're exploring the application and only start using a Harmony with a custom profile after that.

Chances are, you'll otherwise spend a lot of time trying to find a problem in Remote Buddy that's actually not a Remote Buddy problem, but a Harmony training problem.

Best regards, 
Felix Schwarz