Well I have an upcoming itinerary ADL-MEL-SIN-SYD-ADL in Y where I could book all flights under the EK code or the QF code. In the end I booked it under the QF code from the QF website and also offset the discounted fare a little bit more by using points + pay. One of my flights MEL to SIN is actually operated by EK, but I was able to select my seat from Manage My Booking from the QF website. I used the Amadeus PNR from QF and entered it into the EK website to see if it would work - it actually did and I also saw that on the EK website, my seat assignment was also honoured there, so hopefully no nasty surprises at check-in since I picked a very nice seat in the mini-Y cabin on the EK B773.
Difference of about AUD 20 between booking everything from EK, or everything from QF - went was QF because of 100% platinum bonus and SCs.