Hey there,
You should be able to use a Flirc USB with your Harmony Hub without any major issues. Both are pretty versatile when it comes to home theater setups, and they usually play well together.
Regarding controlling Kodi and MPC-BE, you're on the right track. Using the full keyboard option will give you the most control over both programs. That way, you can map specific keyboard shortcuts to actions on your Harmony remote. Kodi and MPC-BE have their own set of keyboard commands, so having full access to keyboard commands will help you toggle between them seamlessly.
Just make sure to do a bit of testing to find the setup that works best for you. It might take a little time to get everything configured just right, but once you do, it's pretty sweet!
Cheers
