This posting is older than 6 months and can contain outdated information.
Remote Buddy is unaware of what you have configured in the Harmony software. It however keeps all eyes and ears open for incoming signals of hardware it supports. This includes the built-in Apple IR receiver.
If you set up an activity within the Harmony software that includes both a PS3 remote and an Apple Remote, the Harmony software will most likely try to build a "Frankenstein" activity that is a mix of both PS3 remote commands and Apple Remote commands. Then, depending on which button you press, it'll send out button presses to Remote Buddy via Bluetooth for those buttons that it put in the PS3 device's "basket" - and will send Apple Remote button codes via IR for those buttons that it determined should go to the Apple device.
Remote Buddy, on the other hand sees signals coming in from a PS3 remote and an Apple Remote - and processes them accordingly. Or said different: in such a setup, the Harmony simulates two different remotes for a single activity - and Remote Buddy consequently also sees two remotes and handles the incoming signals as if they were from two different, separate remotes.
If all you want to do within the activity is control your Mac, then the easiest and best way is to only use the PS3 device in that activity - since all buttons are available for you to configure within Remote Buddy anyway.
If you want to control both your Mac and another Apple device (f.ex. an Apple TV, iPod IR dock, ..) within a single activity, you can still do that, but you'll probably have to do a lot of manual tweaking of the Harmony profile so that the Harmony really sends the button code you want it to send for each button. You'd also most likely want to make sure that your Mac no longer responds to the Apple Remote the Harmony simulates, be it through disabling the IR Receiver in System Preferences - or pairing a different Apple Remote with your Mac.
Best regards,
Felix Schwarz
