Upvote:1
First, make sure that you use the correct six letter/digit reference, i.e. the COPA booking reference and not the Emirates reference (which is probably different) or the ticket number (which is a long string of numbers starting with 176).
Seat selection on code share is always hit or miss. Sometimes it's free, sometimes it can be done for a fee and sometimes, it's not available at all.
You can always select seats when you check-in. To make sure you still have a good selection, check in as early as possible.
In your case, you will probably be just fine: Your check-in window opens 23 or 24 hours before your first leg and since you have a whole lot of flying to do before you get to GRU, you are likely to be one of the first passengers to check-in and grab seats. It's also unlikely that the flights are full, so you should have plenty of good options to choose from.