I have dual zone. During winter days (8am to 7pm), the upstairs zone turns down to 5 degrees cooler than the lower level. There's a second stairs that connects to the kitchen. There's constant cold draft coming down from the second level. The lower level thermostat is in the dining room behind the kitchen. With the cold draft, the heat is constantly running in the lower level. Should I increase the heat in the second level as a solution?

Unless you have a hallway door on the upper level you can close.

The laws of physics are at play here. Hot air rises because its less dense, and cold air sinks because its heavier.

I've found the temprature difference between two floors will be roughly 2-3 degrees F from that alone.

Part of the problem if I understand is the lower levels thermostat is in the path of that colder air coming down the stairs. But even if that was moved... if the stairwell between levels is open and has no door, the heat will naturally rush upstairs.