You can log into the EK MMB, and type in your QF provided PNR.
Of course, EK will issue you a separate PNR from their side, but in the EK MMB, your seat selection will stick.
I had made choices when I flew Au - NZ with EK, always with the QF flight number, went to EK's website, typed in my QF PNR, and the request of/for the J or F seatings, were always there.
Never changed from the option I had made with QF where the booking originated.
I would not dare now try EK Y even SYD - CHC, will pay J/F, but I do realise in your position, OP, that it would too pricey to go J/F on the way to Europe.
No upgrades guaranteed, and when I flew, there were sometimes only me in F!, and sometimes there were empties in J, and there were also times when F was full, and J was a well, but EK "might" do an op up, as mentioned by the others, they are very accommodating when it comes to being on board.
Check in can be hit and miss, I dared to ask for an upgrade in from J to F at AKL, and got rebuffed, but on board was plied with "if I wanted the wines" while on the flight in J.
Maybe without asking, they might give you both J... best of luck though.
Edit: this was when EK still flew between SYD/MEL and AKL.