Unfortunately the EK system is set up so that when trying to upgrade a sector in this way, they apply married sector logic and so you can only upgrade with cash using the outbound or inbound (or up to the first stopover point, as the case may be). Also online they will attempt to charge you a change fee which is specifically waived in most EK fares for upgrades of cabin.

If you do only want to upgrade individual sectors - and I think the way their system is set up is that these don't result in an re-ticket, just a note on the booking and a seat move, so you will only receive original ticketed miles - you will have to either hope for an email special offer, upgrade at the airport (ask at check-in or ticketing) if they are offering it, or at a very last resort on-board (which is likely to be $$$$$).