How to calibrate the input of the measurement system?

The purpose of calibrating the input is to be able to measure absolute level, e.g. SPL or voltage. The calibration can be done in different ways dependent on the features of the sound card (e.g if the WinMLS mixer can control the sound card mixer or not) and the type of measurement you intend to perform. Note that for some sound cards, e.g. VXPocket, a measurement setup is available with nominal calibration settings that can be loaded. To do this, go to Setup->Load... and go to the sound cards section as shown below. Click the  button to load the setup as shown in the figure below.

If the sound card input and output is calibrated, an impulse/frequency response measurement should give an amplification of 0 dB for a loop-back measurement (input directly connected to output). If WinMLS controls the Windows mixer and it is calibrated, the gain should be independent of mixer settings (changes in mixer settings will not change the gain of a loop-back measurement).