question => better source file design

So today I learned a better way to compile multiple files using Makefile and some of the etiquette
that goes into defining such a file which gave me a thought;
since I want to create real networking apps and kernels that will involve many files and many lines of code

"What is a good way to structuring your code and designing it in such a way, that when it comes time to compile using the Makefile
the source code your not lost in all coding nightmare piecing together code file hoping that it will all go together like Lego block?"

using C procedure oriented design so it does not look like it was a high-school programming project