Hi Ben,
I work in the audio team at MathWorks so I thought I'd have a go at this. Yours is a good question, thank you for asking it. The Audio Test Bench is currently still a bit limited in its ability to route input and output signals to the time scope and spectrum analyzer. Specifically, for now it does not provide options to visualize anything else than the first input and output channels, respectively.
If detailed control over live visualization is important, my suggested workaround would be to run the MATLAB plugin in a regular while or for loop, for example following the steps in this tutorial. That way you'll have full control. Along with that, the companion code to this webinar (available here) includes a small example on how to re-create UI controls for live tuning. The function to look at is tuneSingleParameterWithUI.
I hope this helps. If you wanted to discuss more, feel free to reach out to me at gabriele.bunkheila@mathworks.co.uk - my bandwidth is limited but I'll try my best to help.
Gabriele.
