codeshare is really giving me a headache

[G.Y]

so if i'm flying QF8413, aka EK413, booking ref works on both websites, both apps, booked through QF, seats changed through EK, Qf now assigned 2 seats to me (yes i would love to have that) and I don't know which check in desk to go to

 

[AIRwin]

I don't know which check in desk to go to

The answer is in chEcK in dEsK

 

[G.Y]

The answer is in chEcK in dEsK

ahh thanks, that answered all my questions!

 

[Himeno]

Just like with any codeshare, you check in with the airline operating the service.
Qantas is selling seats on an Emirates service, you check in with Emirates.