Sorry, I think I misread your question. I figured you were trying to do a cash upgrade and EK couldn't do it because the ticket was issued by AA. In the case of using miles, I'm not quite sure how it would work if this isn't a codeshare even, but trying at check in, in the lounge, and then on board is probably the best option. However, you'll have to request for each leg separately, and it'll end up costing you more miles, something you probably already know.