Changing how the recorded program display on the My Recordings on your DVR WILL--DOES affect the external HDD. In other words, however you have set your recordings to display on the DVR, will also be how they display on the external HDD. So, if you want the external HDD to display recordings a certain way, you MUST go to the DVR; set-up the display (Alpha, date, etc.) the way you want; then go to the external HDD and they will display as desired.
I don't like that either. It really is irritating, but that's the way it is. Hey, in the beginning the external HDD didn't even display using the folders while the DVR did. External HDD displaying in folders was added in a software update some time ago. I would love for the external HDD to have more independent controls. Let's hope Dish get around to it, but I doubt it.