I install the CLion on a Ubuntu 14.04. I build my first project with help CMakeLists.txt:
Source file:
#include
using namespace std;
When you build under CLion,

It prints the path it sends the executable to the Console:
-- Build files have been written to: /home//.clion10/system/cmake/generated/8bd932b1/8bd932b1/Debug1
To change this File > Settings..., and under CMake settings, enter the desired subdirectory name (e.g., 'bin') in the Working directory field:

(You may require Run > Clean before the new output path is used.)