I haven’t had a lot of success getting the Vero and Harmony to place nice.
I have programmed the Harmony with “OSMC Remote” from the standard profile and tried a number of remote profiles within MY OSMC and none have worked,
I have the IR extender plugged in, although I will admit its not clear which of the 3.5mm jacks it should plug into as they are not marked.
Have i missed a step somewhere? or is the OSMC remote listed in the “My Harmony” app not the right option?
It’s probably best to use something like an Xbox Remote profile as it has more buttons and will let you take advantage of this.
There’s been some discussion re. Harmony and I believe there are quite a few users using one with their Vero.
Sam
The port that is the farthest away from the HDMI port, is for your IR extender. I was also confused about this, as i couldnt find any info on this. Maybe this is something that could be added to the FAQ.
So about your main problem, i also use the Harmony 650. I selected the Samsung TV Remote profile (can’t remember the model and cannot check right now. There is only one samsung profile though) in My OSMC > remotes.
Next, i added the exact TV Model as Device to my Harmony using MyHarmony 
Make sure to to set “i want this device to be powered all the time” (or something along the lines) in device settings.
Set up an activity to your liking.
Most button should work well out of the box, use Keymap Editor for everything else.
I have not ad a lot of time for testing different remote profiles, or even digging into lirc itself enough to modify thing on my own, but the method decribed should be a good start.
I will give this a go tonight, if truth be told i am just looking to replicate the functions of the RF Remote to save me having to have it on hand all the time.