Hello Leon,
The automatic CodeWarrior Makefile generator uses all the files with source file extension within project directory to build regardless of sub-folder where a file is placed.
So if your .c file you are including is not placed completely outside the project directory it will be compiled by default.
However you can explicitly exclude the file from build to avoid compilation of the file. (Click Right on the file -> "Resource Configuration" -> "Exclude from Build..." )
Make sure the include path to the file is set in the compiler input settings/ Includes path settings.
Stanislav