Which lead of a voltmeter is subtracted from which to get the potential difference?
Your multimeter's COM terminal is the one from which measurements are referenced. We usually push the black lead in there.

The 'V' terminal takes the red lead and the meter displays the voltage with reference to the COM socket.

So yes, the meter is displaying \$ V_A - V_B \$ or \$ V_V - V_{COM} \$.