I couldn't understand why you couldn't use the Matlab function block.
Otherwise,run the external m files & capture the outputs of those files into your base workspace & from there you could pass them to your Simulink model by using Input Ports.
To avoid doing this everytime,you can do the following: You can do this using a callback:
1) Open your Simulink model
2) Click "File" -> "Model Properties"
3) Select the second tab, called "Callbacks" in the "Model Properties" window that opened up
4) Select the right callback, and type in the name of your MATLAB function.
You probably can use "PreLoadFcn" callback. The in the "Model pre-load function:" part of the window, type your function, i.e., type loaddata if your function is loaddata.m.
