I'm using it with IAR, Keil, Altium, Proteus and many other s/w
IAR shouldn't detect it. You just make a code modification and GIT detects that some source files has been changed. After that you can upload your changes to repository on web or just commit them locally.
I think, you better google yourself how to use git together with github.
Also, I recommend you to choose template for C development during installation. It will add to ignore list temporary files which is updated all the time you are compiling your project.