Adding custom code

I want to add some custom C++ code to my project. I put my code under my project - despair - source.

The note in that file says:

Your project specific source files and subfolders go into this directory.

Simply add them to this folder and then regenerate your project
Visual Studio Solution/XCode workspace with the Torque Toolbox

Does that mean after I add my files in the source directory I select clean up from the toolbox?

Thanks