I guess I'm down on the system precisely because it makes more difficult the use of credits by two people on the same PNR who each have their own bank of credits. The old system with the certs made that easy. It seems to me that there has to be a solution to this that doesn't involve complex machinations.
On our YUL-YYZ-YQR flights last weekend we had all sorts of uncertainty due to the complexity of this problem where the old system would have made it easy. We decided after dropping our bags off that we would try to upgrade both flights as my wife was feeling ill (we especially wanted the latter segment). YYZ-YQR was J3/R2, so we should have been able to clear, and YUL-YYZ was J9/R1, so chances were good. At the ticketing desk we were told that it was not possible to be upgraded or added to the list AFTER check in has been completed. To her credit, the agent did some asking about this after we left the desk as by the time we got to the MLL the agent there had a message for us that it could be done and was being done after lots of consultation had happened. We needed to get the process completed at the gate in YUL.
At the gate, the agent clears us and gives us J BPs, but we do not know if we are in J on the second leg (why waste credits for a short hop only?), and no way of knowing whether the credits were taken from each of our separate accounts as we had requested. We clear in YYZ too, and all is well. At home the next day, I check my credits and see that new PNR had been created for me and that 6 credits were used from my account, and presumably 6 from my wife's. It all worked, but a mini army of AC employees appeared to have worked on that to make it function. Kudos to them, but this is not simplified airport management of upgrades and if you don't amenable agents you are likely to be screwed. And no, booking separately is not a reasonable answer in my view as there are advantages to being on one PNR.
This can be done better, I think, and it needs to be. I hated the uncertainty and actually wished that I had simply bought the upgrade at OLCI as offered.