Yea, do not manually move the top without the key "ON", this powers up the PTCM and it can 'see' what you are doing, this will keep it from getting confused as easily as when the key is "OFF".
It does not matter if the engine is running or not, just get that PTCM powered up.

On a related note, do not raise or lower the top without the engine running if you are using the button. The spikes and sags on the 12 volt supply can be pretty severe - without the alternator powering the system, these gyrations in voltage can actually damage modules - case in point, I was putting the top up with the engine off back in 2015 when things "glitched" (my battery was almost five years old) and the top froze. I had to put it up manually, and had to re-sync it the next day to get it to move.

But the point is, my seatbelt module died when this happened. For so many reasons, always have the engine running when putting the top up or down with the button.