Unit for downstairs is running fine, but upstairs unit doesn't want to kick on, but outside unit is running (fairly hot though). Tried to re-set, but "cool" just sits there and flashes on the window.

if there is no control of air movement between floors and you have it on cooling then any cold air will go down to the lower floor
or alternately if you have it set on heating all the hot air will rise to the upper floor
where is the system located (upstairs or down stairs ) and where is the thermostat located
to get control close any upstairs to down stairs doors or erect a heavy curtain across the stair well

Soiunds to be a faulkty Tstat or a compressor contactor welded shut.

Replace the thermostat

If you are referring to the secondary pan there could be a problem with your drain line.i would find the drain at the exterior of your home and **** it out with a wet vac..most A.H.Us have float switches or moisture sensors.They will shut down the unit if the drain clogs.

check breaker you may need service.

Most likely the unit is low on refrigerant. You could also have a restriction in the system. You need to put gauges on the unit.

Some of this depends on where the air handler/furnace is located. Most often in two story houses, it's in the attic upstairs, or in a closet upstairs. A duct routes air from the furnace to the downstairs supply duct, so it is a distance from the air handler.
When the unit first initiates a heating cycle, that duct is going to be full of cool air, and the duct itself will be cool. So the furnace has to run long enough to push the cool air out, as well as warm the duct up, before your going to feel warm air at the registers downstairs.

Keep in mind, heat rises. And, your thermostat only monitors the immediate area where it's located. In your case, upstairs.
Two story houses are problematic because of this. And one way around it is to have a damper system installed that distributes the air upstairs or downstairs based on a thermostat located in those spaces. There would be 2 dampers, and 2 thermostats (one upstairs, one downstairs). Each stat would control a damper, and the call for heat or cooling.

Let me know if you would like to consider a system like this, and I can point you to components to use. I've put several system like this in.

Jenny,

Sounds to be a system freon leak. The unit and the stat talk to each other and if the temp is not reached and the unit shut down in a set amount of time it turns on the E-heat. Now there are other facts that could be involved, plugged filters, dirty coils inside and out, etc. Check your filters first to eliminate that problem.

Cold air is denser than hot air, so is harder to move. All vents have some mechanism to regulate flow, so close all of the downstairs vents. Check to see if your furnace fan motor has more than one speed, & set it on maximum. Keeping the fan on all the time will help as well. If all else fails, you may need a more powerful fan motor.