Simple - you need to connect the Audio bezel buttons directly to the master board or to the multiplexer inputs and assign them in the configurator. All you need is a simple plastic (PVC) bezel with buttons and LEDs (full cost about $5-10).
As you can see here: "As the central control unit the SimVimCockpit interface uses a single 16 MHz microcontroller AVR ATmega2560."
I run out of IO ports (inputs for many buttons) on my current ATmega setup, can I connect another ATmega (via USB) to do outputs such as frequency displays?
(I'd rather not mess with multiplexing as it adds complexity.)