Although AudioTools is basically designed to support one microphone input (left channel or channel 1) for the acoustic functions, and at most two inputs for things like Transfer Function and some of the Line Input tools,  we do provide support for mapping the main input channels from other channels when you using a multi-channel audio interface. 

To use a channel other than channel one for the microphone, connect your multichannel interface, and navigate to Settings->Channel Mapper. From here, you can select the channels from your interface for both the microphone source and for the line input source.

Note that if you are using uPrecisionMic, uTestMic2, iAudioInterface2, or the built-in device microphone this option will not be available.