I have a similar size house and furnace set up. However I don't experience the temperature variations you are seeing.

What is floor area of the first and second floors? Does the first floor have an open cathedral ceilings going up to the second floor? Do have returns on each floor and are they connected to each other?

i do have a high open cathedral type den...the square footage upstairs is approx 3/4 of what the downstairs is...i do have returns on each floor but don't know if they are connected...

It sounds like the heat from the first floor is rising up through the cathedral ceiling to the second floor. You should look into installing a fan at the highest point to circulate the air.

Set the temperature for the second floor to 70 degrees. The second floor furnace will probably never turn on. I suggest using temperature set backs during sleeping hours.

Which way is most efficient depends a little on the house design. If the ductwork for the upstairs is in a vented attic and the downstairs is in a more controlled space (like a basement), then what you have is the most efficient setup.

I basically intentionally do what you are doing because my downstairs unit is more efficient and the ducts are all in conditioned space. The upstairs winds up being cooler than downstairs which works well because we like to sleep in the cold.

It is generally more efficient to run a furnace for longer periods of time so I wouldn't worry much about that. But if you are using a heatpump and this setup pushes you into backup electric strips, you're killing your efficiency. So the details of your systems is important.

Don't confuse efficiency with economy.

It's not that it's desirable to run a furnace for long periods of time, rather that it's inefficient to run it for multiple short cycles. If your heater will run 30 minutes per hour, two 15 minute periods is more efficient (more heat for the buck) than six 5 minute periods. However, if by comparison your heater runs 45 minutes per hour, it'll cost you up to 50% more.

For a given furnace, using longer cycles is more efficient. But, longer total running time is more expensive.