Rheem furnace ,RGGE Contour ,communicating ,modulating , 2 stage

Without the thermostat telling it, the furnace has to guess how much heat you need, and those guesses may not always be right. The thermostat will know how far you from your target temperature and know which stage you need to be using. That means a thermostat wired up for both stages will heat up faster when you get back from vacation, and the temperature stays more constant all other times.

I hope the 90K is the output or it's truly undersized! Even so, it's quite common to oversize furnaces beyond the calculated heat loss by 20-30%. It's also possible the heat loss calculation is low, it's really just an estimate, and part of why the furnaces are oversized. Even if it is undersized, it would not significantly alter your energy costs. Costs are dependent mainly on the home's overall insulation and the furnace efficiency, the capacity and running time is not a big factor.

Changing ductwork will better distribute the heat, but if more heat is leaking out than the furnace can generate, it will not help. While a larger furnace will better heat your home, it will not help your energy costs. If your costs are out of line for your type and size of house in your area, then more heat is being lost than is typical. In the long run, you are better off preventing heat loss than generating more heat.

There are energy consultants in most areas that have the proper tools and equipment to advise you where most of the heat is being lost and what could be done to most effectively reduce heat loss.