It's hard to remember what all was supported in 2008b, and I'm also not a Simulink expert. What does your MATLAB script really do? If it's just defining input data, then that can be handled as a purely Simulink thing, and you can generate code from your model using Real-Time Workshop. If it's implementing some kind of algorithm and calling sim(), then what you probably want to do is generate a library for your Simulink model and then write a driver for it in C that implements what your script is doing and calls into that library. If the algorithm in your script is really complicated, you might want to use emlc (I think it was still "emlc" back then--now it's called "codegen") to generate code for it, but you'll have to do some work to use coder.ceval to call into your library.