It's definitely possible cause I've done it before on a VA operated NZ coded/ticketed flight from Christchurch to Brisbane. You just end up paying over the phone using a credit card...
It's possible to do it at check in but should be the same on the phone with EY tickets as it is for NZ tickets.
I'd keep trying on the phone and tell them you want to pay now otherwise you'll be waiting till checkin and if any seats are free then people can buy them at the check in desk.