For information setting up your harmony device to work with flirc see this article
This article describes how to add customs buttons to your harmony remote which you can then map to a custom keyboard combination on flirc (e.g. to open an app).
Open the "myharmony" app (available here: http://myharmony.com/)
Select the "Buttons" tab then click the drop down menu and select "Flirc Media Player"
You then be presented with a virtual picture of your remote control (in this example I have a harmony 300):
To determine what buttons have functions paired with them hover over the button with your cursor. If the button is not assigned then the software will say "Nothing (Not assigned)". Below is an example of hovering over the keys:
(Apologies, embedding wasn't working)
If the remote button has nothing assigned to the button, when it is pressed it won't emit a signal (so Flirc has nothing to respond to). If we want to add a custom command then we'll have to add a signal.
I'm choosing "Favourite 1" button to program in this example, as you can see it has nothing assigned to the button:
Click "Teach command" in the bottom right corner of the window:
Then we want to "Add a missing command", in the case i'm adding a button to open an app called "Kodi" (hence the name of the new command):
The software will guide you through the steps of adding the new button. For my button I used an old blu-ray player remote I had:
If successful you should see a message similar to this:
The new command will now show up on the side bar (highlighted below):
Then drag and drop this new command onto the button you want (in this example "Favourite 1"):
If successful, when you hover over the button it will show the command you dragged onto it:
Repeat this for as many commands as you need to add then remember to sync the settings:
Now you can program that button using the Flirc GUI