Lyman.
The Main Bat is only connected to a live bus when no other electric source is available and Bat Switch 'on'. Therefore it is not discharging unless there is a power failure.
The APU Bat is charged from the F/O's Instrument Bus. This can be powered from a variety of sources, not just the APU. EG. Ext power, Eng Gen. After starting the APU, the APU Bat does nothing but sit there and get recharged. (Unless towing without APU/ENG GEN in which case it powers the Nav lights)