First off, heat rises. Next, the partial underground situation lowers the temp considerably; the underground temp here is 55 degrees, possibly lower in your location.
A couple of things you might try:
Insulate the lower rooms with 2" foam board to defeat the ground temp, to get really serious you would need to insulate the floor also. This can be done with carpet and pad or by raising the floor with 2 Xs, insulating between the sleepers, then use subfloor and vinyl or laminate.
Re-balance the air flow from the furnace. You have a good brand and, with the 2 stages, it should be very efficient. You will need dampers in the trunk line to regulate increased flow to the lower level.
Get rid of any flex-duct and replace it with metal pipe and sleeve insulation.
Run your fan on low speed constantly to keep a mix of the air and temperature you have. Is the lower level in the North to West quadrant?
Try any one or all of these remedies and accurately measure the difference in temp, upper and lower, and before and after. Let us know how it works out for you.