The Introductory Guide has some details about tailoring the profile for C, I would suggest first looking at the demo apps in c/examples.
Compile and step through encode & decode and you should get a feel for how to work with the SDK. One thing that is *very* confusing right now, in the file fit_config.h you need to redefine the constant FIT_LOCAL_MESGS to something larger, say 16. We will get this fixed up so the example is nicer out of the box.
The other thing I would suggest is look in the examples folder and examine the .csv for file types pertaining to your application. There are a lot of fields and messages to digest and the examples are useful to see how they fit together.