Add our own files and directories for compilation

Hi,
I am working on a company which develops video games and which one is inspired by STK.
They want me to create the online multiplayer mode and before to add my code in their own project, they want me to introduce it in the STK code.
So here is my issue, I don't know how to add my files in the autoconf scripts for including them in the Makefile autogenerated.
I have tryied to use update_file_list.sh to add my files in the CMakeFile.txt and apparantly it works, but I don't know how to autogenerate a new Makefile from this new CMakeFile.txt.
I have tryied to create a build directory and Cmake but I really would like to go on with autoconf and Makefine from root directory.
If you have the answer, thanks a lot.
Bye
I am working on a company which develops video games and which one is inspired by STK.
They want me to create the online multiplayer mode and before to add my code in their own project, they want me to introduce it in the STK code.
So here is my issue, I don't know how to add my files in the autoconf scripts for including them in the Makefile autogenerated.
I have tryied to use update_file_list.sh to add my files in the CMakeFile.txt and apparantly it works, but I don't know how to autogenerate a new Makefile from this new CMakeFile.txt.
I have tryied to create a build directory and Cmake but I really would like to go on with autoconf and Makefine from root directory.
If you have the answer, thanks a lot.
Bye