The Harmony has a built in profile for XBMC that's been fine tuned to work perfectly with flirc. Make sure you have the at least firmware version 2.6. You can fire up the GUI to check the firmware version.
To upgrade to the latest firmware, grab the latest download on the website. Go to advanced, and force a firmware upgrade.
Now that you have the latest firmware, install the XBMC-Flirc profile on your harmony. You can find it here:
That's it, your flirc will just work with your XBMC profile. If it's not, fire up the GUI and make sure built-in profiles are enabled.