Steve,
If you are trying to perform dual-channel measurements (e.g. frequency or impulse response), I would point you to the tutorial on the blog for reference.
Frequency Response Measurement with Electroacoustics Toolbox 3
Why can't you use the output of the Duet to use the built-in test signals? Perhaps, a more detailed description of what you are trying to do, and how you would like to set it up, would help us zero in on a suitable solution.
Ben
