Connect the measurement microphone to sound card input channel 1 (left).
If you are using a sound card with stereo input, connect the sound card output ch. 2 to sound card input ch. 2. This internal loop gives the reference measurement.
If you are using a sound card with mono input which most microphone inputs are, go to Measurement->Settings... and select 'Generator' as shown in the figure below. You should then in step 7 correct for the sound card frequency response and delay.
Note: This method may not be as stable as the metod using ch. 2 as reference when doing repeated measurements (sound card dependent).
Connect the sound card output ch. 1 (left) to the sound system input. Left and right ch. of the sound system should be measured separately.