Change the layout in `keymap.c` then run `make xd60:yuuki`. The compiled file will be located in `.build/xd60_yuuki.hex` relative to the project root. To flash it onto your keyboard, use whatever program works on your OS. I personally use `dfu-programmer`, and run:
Upper row is default layer, bottom row is function layer. I Didn't include the symbols, such as @,# or $, as their placement is just as you'd expect it.