The “Makefile Project with existing Code” interface is not fully compatible yet. To create your Makefile project, check the “Create a STM32 makefile project” section in http://www.openstm32.org/Creating+a+new+project?structure=Documentation
While creating your project, you can change the project location into your source location. Don’t forget to select the “Ac6 STM32 MCU GCC” toolchain, it adds a window to select or create your board.
Hope it helps,