Till date I still do not really understand what the \'best practice\' is for doing this for a CMake project with many subdirectories.
Say I have a project hierarchy
In your case there's no need to use add_subdirectory since you have only one target which is created in the root CMakeLists.txt. You can simply write this:
add_executable(myProg
SubD1/Source.cpp
SubD1/SubSubD1/Source2.cpp)
Use add_subdirectory for subdirectories creating their own targets so there's no information to pass upwards.