Upgrades are cleared two ways....in advance, in the 'black box' process and from those on the standby upgrade list, at the gate, usually just prior to boarding.

The in advance process is available until some time not too far before the flight...think it used to typically be about 3 hours. Not sure if that's changed. It is supposed to run upgrades at all the elite upgrade windows, and will clear folks, assuming upgrade space is availble. It also runs, supposedly, every time an upgrade-eligible passenger checks in - as a gold and plat, I have occasionally checked in in economy, and found myself upgraded because the BP shows a seat in F. It's been a while, but it happens.

Checking in won't affect your ability to clear an upgrade in advance (the only disclaimer I know of to this is if you have another person on your PNR, it will split, so you will be on the list as two individuals, as opposed to a party of 2 - this has advantages and disadvantages, depending on your preferences). But you can still be upgraded in advance after check in. I've also had that happen several times in the last few years.