To use a QMK based firmware, you might want to install a QMK bootloader. The PCB exposes 6 pins for ISP(In-System Programming), and they are located just under the ATMega32U4 chip. From left to right, the pins are `VCC`, `SCLK`, `MOSI`, `MISO`, `RESET`, `GND`. The `GND` is the square one. You could program the flash with any AVR programmer, or a Raspberry Pi with `avrdude`.
See the [build environment setup](https://docs.qmk.fm/#/getting_started_build_tools) and the [make instructions](https://docs.qmk.fm/#/getting_started_make_guide) for more information. Brand new to QMK? Start with our [Complete Newbs Guide](https://docs.qmk.fm/#/newbs).