Download or clone the whole firmware and navigate to the keyboards/atomic folder. Once your dev env is setup, you'll be able to type `make` to generate your .hex - you can then use `make dfu` to program your PCB once you hit the reset button.
Several version of keymap are available in advance but you are recommended to define your favorite layout yourself. To define your own keymap create a file in the keymaps folder named `<name>.c` and see keymap document (you can find in top README.md) and existent keymap files.