"I'm not sure I follow your method given that the heating and cooling were bundled together....Do you actually mean total energy divided by HDD or CDD?"
To illustrate the method, assume a house that is heated by an electric space heater and cooled by an electric air conditioner, both of which are connected to the same electric meter.
The way to seperate out the appliance useage is to observe the meter during a period of time in which only one appliance is used and observe the number of DD for the same period. In my part of the world, the month of January never requires any air conditioning. So, if you take the meter reading for January and divide it by the cumulative DDs for January the resulting quotient would be the heating unit's DD factor (kWh/HDD).
The same could be said for the cooling load. In my part of the world, the month of August never requires any space heating so an air conditioning DD factor can be determined by using the procedure outlined above for August to get the air conditioning unit's DD factor (kWh/CDD).
Now, everything being equal (thermostat setting, appliance efficiency, building insulation, occupants etc.), the DD factors will remain reasonably constant and you should be able to use them to estimate the mixed heating and cooling consumption for any other month by using the relation:
Total Mixed Load = (HDD x kWh/HDD) + (CDD x kWh/CDD)
Note, if you undertake energy savings measures, you will need to determine new DD factors to account for the changes.
"And won't the HDD/CDD factors suffer the same proportionality problem after improvements?"
The HDD/CDD ratio is not used in the calculation.