How do I use the auxiliary input channels in CMT?

The Ain settings are implemented as follows:

The output of analogue channel data are activated by the output mode.  E.g.:
#define CMTOUTPUTMODE           CMT_OUTPUTMODE_STATUS \
                            |   CMT_OUTPUTMODE_CALIB
//                          |   CMT_OUTPUTMODE_ORIENT \
//                          |   CMT_OUTPUTMODE_POSITION \
//                          |   CMT_OUTPUTMODE_VELOCITY \
//                          |   CMT_OUTPUTMODE_AUXILIARY \

The sensor will then output both Ain channels automatically. By setting the output settings, you can DISable analogue channels if required. So you should not activate the AUXILIARYMODE settings.
#define CMTOUTPUTSETTINGS       CMT_OUTPUTSETTINGS_TIMESTAMP_SAMPLECNT \
                            |   CMT_OUTPUTSETTINGS_ORIENTMODE_EULER \
                            |   CMT_OUTPUTSETTINGS_CALIBMODE_ACCGYRMAG \
                            |   CMT_OUTPUTSETTINGS_DATAFORMAT_FP1632\
                            |   CMT_OUTPUTSETTINGS_POSITIONMODE_LLA_WGS84 \
                            |   CMT_OUTPUTSETTINGS_VELOCITYMODE_NED \
                            |   CMT_OUTPUTSETTINGS_COORDINATES_NED
If applicable, note that the FP 16.32 format applies to all output that is usually given in 4-byte floats. Keep in mind that the analogue channels are unsigned shorts which are therefore not affected by the FP16.32 setting.

Also refer to the User Manual of your device for further information on using the auxiliary channel.