I don't know if this is particular to my project, but I find that I can include Matlab generated files the same way as you would normally include anything else.
I copy my generated matlab source files (.c and .h) into my project directly, and then I have to specifically add them to my project. ( I wonder if that has more to do with the IDE I use though).
Then, in main.c that you create, just add the line #include "yourGeneratedFile.h". Within main.c now, you should be able to use whatever functions were created by Matlab.
For instance, in an example:
within main.c, include the header file and use the function you need
#include "SPIUARTDemo30f.h"
//further down in the file
SPIUARTDemo30f_step(); //using the function I asked Matlab to generate
SPIUARTDemo30f.h and SPIUARTDemo30f.c are the generated files from Matlab:
within the .h you'll see
extern void SPIUARTDemo30f_step(void);
and, if you look at the .c you'll find:
void SPIUARTDemo30f_step(void)
{
/* lots of code */
}