With the relatively new ability to pick upgrade seats from the seat map, I've kept automatic C+ upgrading off; I now buy the tickets, and then look at the seat map for C+ options that are
actually upgrades.
This has worked pretty well for my most recent trip purchases.
Since DM/PM get the chance to do this at any time before the trip (assuming availability) it's not much risk that I'll miss the upgrade because I waited to pick a seat, but were I GM or FO if I wanted to be sure I'd set an alarm to look at the seat map as soon as my upgrade window opened.