The kernel header files are located in /usr/include/linux/*, /usr/include/asm* and /usr/src/linux.
BtW: Why do you want to include certain third-party header files in your program? Just make them a requirement for the user before he installs/uses your program. You could always make the additional files available as a separate package.
If you mean by "include" the #include-directive, then you will be including kernel header files for sure in your program, if you use glibc as your c-library.
I'm not a lawyer so I cannot say if your program will be GPLed by this procedure.