Hi. If your audio inputs are separate connection and not in your camera in-->sdi out --->capture card so the sdi vmix input will carry audio together,you need to do routing separate your audio.
How many audio inputs you have? Do you use all the 4 outputs? A way to do this you need is to select an audio bus (other than the master) for any of your audio input you need to capture and then select one output 2-4 from it`s cog settings instead of master to record all the buses. Then select this output into multicorder and wav enabled (if you select mp4 multi/recording and not wav enabled mp4 format can handle 6 channels so at maximum MAB and be aware for this limitation or use vmix avi and then see how to proceed further for post production) and if you need also to record the actual camera sdi out sound,you have to select in multicorder the Audio-->input or if you need the pgm audio for your raw camera record you select the Audio-->master
Also see in the audio inputs the setting called "channel matrix" to do other settings needed. For example if you dont mind to record mono your audio inputs, you can do via the channel matrix, for example the Audio 1 input to be recorded in BUS A left channel,while the Audio 2 input can be recorded in BUS A right channel.
Test and see what fits better for you