Just received my QR code, just 2 days after my application.
Now I can confirm: In the Covid Certificate Section, please submit your EU Digital Covid Certificate (1 page only) twice. For First Vaccination and Second Vaccination as well.
Same QR Code for 1st and 2nd Vaccination.
For Date of 1st Vaccination: e.g. 10/June/2021.
For Date of 2nd Vaccination: 11/June/2021.
Hope that helps.