The most reliable way to book award seats is to ring EK and ask. Over christmas I had no luck on the website and also expert flyer was showing no availability. I called emirates and was able to upgrade straight through MAN - SYD. For the return I called EK again and managed to upgrade straight through as well. I was on Y flex + tickets and had to move my return flight one day to the right to get the upgrade.
I wouldnt bother using the auto upgrade feature it is more a benefit for EK than passengers. It is possible you could get upgraded at the airport and miss out on the CD and also the lounge if you wasn't gold.
Is there not a minimum stay in MCT?