The FFT C model and FFT MEX function are single-channel models that do not directly model multichannel FFTs. However, it is very simple to model multichannel FFTs.
By definition, a multichannel FFT is equivalent to multiple identical single-channel FFTs, each operating on different input data. Therefore a multichannel FFT can be modeled by running a single-channel model several times on the input data of each channel.
For the FFT C model, the example C++ code provided, run_bitacc_cmodel.c, demonstrates how to model a multichannel FFT. This example code creates the FFT state structure, then uses a loop to run the model on each channel's input data in turn, then finally destroys the state structure. For the FFT MEX function, call the function on the input data of each channel in turn.