The following method may not be safe depending on the ability of the HV supply to deliver short-circuit power. Risk mitigation is added at the end, but be aware, that depending on the size of the HV supply's output capacitors, the operator could receive a lethal strike, when doing these measurements carelessly.
Connect your multimeter in current mode 1 between output side A and GND.
If it measures 0, this side is GND or isolated.
If it measures 1 mA, this side is positive with respect to GND.
If it measures -1 mA, this side is negative with respect to GND.
If side A was reading 0, repeat for side B.
If both sides show 0, then the output is isolated, which means that you can choose if it is negative or positive by connecting one side to GND.
1 The moment when you connect the multimeter to a differential voltage of 30 kV, the output caps of the HV suppl discharge through the multimeter in much the same way as an ESD strike. However, the total strike energy can be higher than for ESD and damage the meter. To avoid this, it would be safer to first short-circuit the measurement path with a wire, then connect the meter, and then remove the short-circuit.