The overall heating system efficiency is the ratio of the thermal heating energy divided by the heating fuel.
I recommend using the predefined summary reports, specifically the Energy meter summary. Within this report, go to the table, "annual and peak values - other". Here you will find the EnergyTransfer outputs. Depending on your HVAC system, you may be able to simply grab one of the Heating:EnergyTransfer outputs, or the HeatingCoils:EnergyTransfer output.
I think HeatingCoils:EnergyTransfer is the best option, but you may have other means of heating not included on this meter (baseboards, radiant, etc.) You will have to check the .mtd file to be sure it captures everything.
Further, if you have heat recovery, then you will need to add the HeatRecoveryForHeating:EnergyTransfer output to the HeatingCoils:EnergyTransfer.
For the energy usage, you should be able to sum all heating fuel energy from the ABUPS end use table. The overall heating system efficiency is the sum of the Heating:EnergyTransfer outputs divided by the sum of the heating fuel consumption.
best,
Greg