Don't "check-in" until you're finished with upgrade attempts.
In other words, don't check-in until "this" is the seat you want.

You can upgrade into MC at 24hours, but you can't upgrade tp F until 6 hours.
This presents an issue for those with MC tickets hoping for F ...
1)... do I hold out trying to upgrade until the 6 hour window when I can try for the seat I really want
...or...
2)... do I upgrade to MCS at the 24 hour window so at least I'll get something. And try upgrading to F later.

For those choosing option #1 it's easy.
Wait until the 6 hour mark and check-in. Grab that "double upgrade" to F if it's available. Sit in MC if both F and MCS are full by now.

For those choosing option #2, it ain't so easy, but they may get the consolation prize of MCS
At the 24 hour mark, try the single upgrade MC->MCS. Don't check-in yet because this is not my final upgrade attempt.
At 6 hours, check-in. Grab the 2nd single upgrade MCS->F if it's available. If not available at least you got an MCS upgrade for your extra efforts.