How to deploy a MATLAB + Simulink app

Hi all. Relative MATLAB newbie here. I inherited a mixed MATLAB/Simulink application that appears to both run a Simulink model from a MATLAB file and run MATLAB files as S-functions from Simulink. I would like to deploy this app as a Windows executable. After researching and trying a couple of things, it seems that I need to do two things:

1) Create a MATLAB application with the MATLAB compiler

2) Use the Simulink Coder to generate C code, which then must be compiled separately

Am I correct in my assessment? As I am not an experienced application builder, I am unsure how to link the two parts of the app. Also, do I need to compile each of the S-functions separately in MATLAB or does the Simulink Coder generate C code from the S-functions?

Thanks, -Jamie