I don't understand. To do that you just need to pass the subdir with your CMakeLists.txt to add_subdirectory(). Exactly which problems did you experienced?
Looking at it now, I wanted to copy files into the build folder after build step was done with add_custom_command() with copy_if_different and with target TARGET <project> POST_BUILD, but when I would put that in a subdirectory it wouldn't work because there was no target.