Well, you look up the format of executable files under your operating system and find the parts of the program that you want to edit, like the code segments. Then you write the code you'd like to run, let your compiler translate it into the appropriate binary format (or you do this step by hand) and write it at the right spot. You have to be careful if addresses change (because you changed the size of the code for example), then you have to to the linker's job again.