I don't know fully what's they are doing. But here's my workflow with watchtower.

I have a cron task that runs watchtower every day on monitor-mode and only-once one time a day. That creates a list on what containers can be uograded. They using shourrr (it's already integrated with watchtower it's just an environment variable to do this) I send myself a message to my phone informing me of what updates are available. If I see fit to upgrade everything I just run watchtower once without monitor mode to upgrade all. I have pendant to automate this last part in a way that I just answer to the bot that's informing me of the updates and should apply the command without having me ssh into the server. But as for now I have to ssh and run a script I have at hand to launch the upgrade with watchtower.

There are some problematic containers that I don't want to upgrade this way. For those I have their compose files version locked and I upgrade them manually when I want.