Configuration suggestions for unique building?

Okay, so the building in question is an old 2-story from 1877.  One furnace with a trunk that runs along the length of the 1st floor ceiling & ducts that feed upstairs & downstairs.  Downstairs is my father's music store that has very limited, specific hours of operation.  Wed. - Sat, 2-4pm.  Upstairs is a residential space where my wife & I currently live.  

We installed a new furnace this summer & have been working to dial everything in.  The issue is that it stays MUCH cooler downstairs than upstairs in general, so when the shop is open & we turn up the heat down there, we're roasting upstairs.  I saw a 12º difference last week, which is when we ordered the Flair vents.  We now have 7 vents and a puck.  

The way we've been running the schedule is with our Ecobee thermostat & remote sensor.  The sensor is downstairs, thermostat upstairs.  We have the schedule set to read only from the remote sensor while the shop is open.  With the introduction of the Flair system, I'm not exactly sure what the best way to program all of it would be.  I'm pretty sure the puck should remain upstairs since that's the "room" that the vents can control airflow into.  From what I can tell, there's no way to schedule a simple opening / closing time for the vents.  What may work best is to un-pair it from the Ecobee entirely & let the puck's sensor control the vents, but I'm just not sure.  

Thanks for any input!