Why not set both systems at the same temperature so they don’t end up fighting one another? I think what you’ve described is a complex multi-zone system where it’s hard to predict what’s optimal. You may just have to experiment. Are these systems using different energy sources?

A Programmable Thermostat Could be Your Solution.

https://www.newcentralairconditioner.com/

Installing a programmable thermostat in your home will let you run a scheduled heating and cooling program without having to remember to manually change your settings throughout the day.

Most programmable thermostats are able to automatically adjust the heating temperature in your home up to six or more times per day. You can also manually override the automatic settings if you need to at any time without interrupting the daily or weekly programming.

A programmable thermostat offers such ease of use, that it's easy to set your home's temperature lower while you are asleep or during the day when you are at work.

In the summer months, raising your home's cooling temperature to over 78 degrees Fahrenheit for eight hours per day — a typical work day — can really make a difference in your utility bills.

When programming your thermostat, just take into consideration your daily schedule. In the winter, do you like to sleep in a cool house? If you like your home cooler at night, set your thermostat to a lower setting about an hour before you actually go to bed so the house starts to cool down. Prior to waking up, you might want to set the thermostat so the heat comes on approximately two hours before you actually get up so the house is nice and warm.

You should also consider adjusting the thermostat anytime your house is vacant for four or more hours per day. Typically, adjusting temperatures 5 – 8 degrees (down in winter, up in summer) can help save energy if you are going to be away from home for several hours.

kudzu9 - I'm afraid if the HVAC is faster to heat the rooms, the baseboards won't ever turn on. And if they never turn on, that might be the more efficient way to heat the house. Both system run off gas.

mike_home - Gas Furnace heat and AC, All bedrooms are on 2nd floor, Preferably 70deg in the winter and ~80 in the summer.

Marc Well - Ecobee's on each system. This was a challenge because the Goodman GMVC96 has a variable fan and the ecobee can possibly do three speeds (pick one only). Unfortunately the Goodman Comfortnet is $400 which we didn't want to spend the money for just so the thermostat and furnace can relay info back and forth. So I selected the furnace to control the fan.

I think the idea is that the Navien hot water be the main source for heat and the HVAC is the gravy, it'll fill in the missing heat on those really cold days...

I recommend you turn off the baseboard heating for the second floor and use the Goodman furnace for heating. The costs of operating the furnace to heat the second floor is going to be less than the boiler. I see no advantage of having two systems provide heat at the same time.

Set the temperature at 70 degrees if that is a comfortable setting. If you want to save some money set back the second floor temperature during the part of the day when you are not occupying the second floor. I think setting back the temperature while sleeping is a good idea.

The first floor should also be set to 70 if that is the comfortable setting. You can set back the first floor during sleeping hours.

I'd set the Goodman temperature one or two degrees above the Navien's "upstairs" setting. The Goodman would then act as a backup in case the Navien wasn't able to heat the upstairs sufficiently.

-- amateur