There are effectively two upgrade lists -- the CPU list and the gate list.
You can only see the gate list and it is not used until close to departure. So you have plenty of time to get n the gate list. The pre gate upgrades are handled from the CPU list and you can not see it and do not need to be checked in to be on the list. There has never been clarity on if the prioritization on the two lists are identical UA seems to suggest they are the same but real world experience seems to suggest some minor differences.