You need to be familiar with the Harmony app, but I can help you if you didn't understand me on that.
As for the remote.xml, it's a great way to associate commands with certain keys on the remote.
I'm using a zotac nano AD10 that I bought back in 2012. I never used the external IR receiver.
Right now, I'm still on LE 8.2.5 using my Zotac as a device in my Watch a Movie activity.
To test LE 9.x, I created another activity called Watch a Movie 2. In it, I simply replaced the zotac with an MCE device which I called Microsoft 1040.
I programmed the remote just like it was a zotac (for the keys and window, removing unnecessary MCE commands that didn't apply to the zotac).
Some keys can be different (like Back instead of Return), but just use common sense.
Now, MCE codes won't let you turn ON the zotac from boot. So I needed to add the zotac as an extra device to my Activity just for turning it on.
I left everything else unprogrammed for that zotac device so as not to cause double keypresses. If you prefer using that external IR receiver, you won't have to do this (maybe?)
Anyways, I'll be staying on 8.2.5 until something pisses me off, but at least my Harmony is all ready for 9.x LE versions now.
Good luck