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If you have the Plex device added to your Harmony, you're most of the way there. That device is actually a collection of 10 different Apple Remote ids, giving you about 60 remote codes to work with. You'll need to turn on support for multiple remote ids in Remote Buddy, and let it detect each of the 10 remote ids by pressing buttons on the Harmony. This list of which Harmony buttons correspond to which buttons on which remote id will be helpful: https://secure.iospirit.com/support/forums/remotebuddy/singlethread/13590/
Once RB is aware of all ten of the remote IDs, you can go into its preferences and map any button on the Harmony to any action you want for each behavior. I only have one activity in the Logitech setup to control the computer, but you could set up separate activities for different programs. You'd need each activity to send a unique code as it starts and have RB's global mapping set to launch the appropriate behavior when it sees that code.
