difference between CMake file syntax and CMakeLists.txt at kdevelop?

[Krzysztof]

I tried to set some variables (e.g. CMAKE_CXX_FLAGS_DEBUG) in 
CMakeLists.txt file but I'm afraid kdevelop doesn't recognize it. After 
I generated this file under cmake-gui, kdevelop had commented the line
set(CMAKE_CXX_FLAGS_DEBUG)

What's wrong?

-- 
Regards
Krzysztof J.