If you want to flash a microcontroller to be your keyboard you can use QMK for that. You can even use the QMK toolbox to do it, which is a UI that helps you to flash/compile your keyboard mapping and even to already select the kind of bootloader that you use to flash your microcontroller.
If you want to flash a recently edited or something that you changed recently on the configuration file, you might need to use the command line for that. There was when I questioned "How will I do it for the Elite-C?".
I use Arduino Pro Micro for almost all keyboards that I built, but because of micro usb not being the best when it comes to durability, I choose Elite-C to be the microcontroller for one of the keyboards that I created.
So here's how you flash it:
Arduino Pro Micro:
qmk flash -kb sofle -km default
With that, the keymap will compile and it will ask flash the Arduino, if you connect reset to ground, it will accept the flash.
qmk flash -kb sofle -km default -bl dfu
With that, the bootloader used will be DFU instead of avrdudes (used for Arduino Pro Micro). You don't need to do anything in the board to flash it.
This is simple and easy, but I took a while to find this info, so here it is :D
For more info about QMK and flashing, go to their wiki page https://github.com/qmk/qmk_firmware/blob/master/docs/flashing.md