Basically, progress clocks are used to track any task that takes more than one action to perform. Want to seduce the duchess a the ball? Progress clock. Research a special alchemical formula? Progress clock. It works both ways too. A progress clock can track failures leading to the guards being alerted while you are trying to steal the charts from your rival's ship. AND you can have more than one of them running at any given time.
Now 7th Sea already uses something like this buried in the mechanics. Story steps and Villainous schemes could EASILY be represented by progress clocks. The whole idea of timed events in action sequences feels like it would map very closely to the way progress clocks can be used as well.
But with all the hand wringing about dramatic sequences, it strikes me that progress clocks might be a missing ingredient that makes the whole thing click that much better. Consider if your players go into a dramatic sequence with three progress clocks running: 2 related to goals the players have set, and 1 detremental to their goals. The players have to spend raises to tick off incriments on the two goal clocks as well as spend them to stall the third clock. Meanwhile, the villain could have his own clock as well.
I don't have much more than that right now. This is a VERY half baked idea. But it feels like one more nice tool that could be added to the GM's toolbox to make the game work for him. I'm considering elements that could give them features ala the "death spiral" (bonus dice, add to danger pool, etc.).
So I thought I'd throw this out there and see where other people take it.