Hello James,
When you generate the executable it also generates the source files (see the below doc link). http://www.mathworks.com/help/rtw/ug/files-and-folders-created-by-the-build-process.html
With those source files you can bring them into Visual Studio and add additional source files around the ones that you generated you can build a new executable that achieves what you want. Please see the following link on relocating the source files to an IDE such as Visual Studio: http://www.mathworks.com/help/rtw/ug/files-and-folders-created-by-the-build-process.html
For more information regarding building in Visual Studio, please check out the following documentation: http://www.mathworks.com/help/rtw/examples/creating-a-microsoft-visual-studio-solution.html