If you create a dual recording (i.e. you capture channel A and channel B) and want to disable the audio on one channel, please take following steps:
Select the tab 'Configuration', then the tab 'Encoding & Layout' and the subsection 'Encoding Presets'. Choose what you like to record for which channel.
After you selected the desired recordings, select in the table 'Encoder Presets' the corresponding Preset and save the changed channel. You have to save the preset otherwise your settings will not be set after a reboot.