You could try to add two more columns to your input system matrix B,

i.e. B(:,2) = data_input_2   

      B(:,3) = data_input_3    

Hope that helps you think for the solution. Post a sample of your code/screenshot to get more help 

https://m.youtube.com/watch?v=pS1KyGQnpy8

Use state space model in model structure 

 If the measured data is FRD, you can use SSEST command to obtain the model fit